From a98d0c5be48c97885bb71c3fd2b10affc5901f42 Mon Sep 17 00:00:00 2001
From: Noah Callaway <noah@apsis.io>
Date: Mon, 9 Mar 2020 21:55:58 -0700
Subject: [PATCH 01/30] Issue 818: Add legend to map view

---
 src/components/main/index.js         | 10 ++++-
 src/components/map/map.js            |  5 +++
 src/components/tree/legend/legend.js | 67 ++++++++++++++++++++--------
 src/components/tree/tree.js          |  6 +--
 src/reducers/controls.js             |  8 +++-
 5 files changed, 72 insertions(+), 24 deletions(-)

diff --git a/src/components/main/index.js b/src/components/main/index.js
index f6c8b5deb..8aa27ff41 100644
--- a/src/components/main/index.js
+++ b/src/components/main/index.js
@@ -77,6 +77,14 @@ class Main extends React.Component {
   toggleSidebar() {
     this.props.dispatch({type: TOGGLE_SIDEBAR, value: !this.props.sidebarOpen});
   }
+
+  shouldShowMapLegend() {
+    const showingTree = this.props.panelsToDisplay.includes("tree");
+    const inGrid = this.props.panelLayout !== "grid";
+
+    return !showingTree || inGrid;
+  }
+
   render() {
     if (this.state.showSpinner) {
       return (<Spinner/>);
@@ -133,7 +141,7 @@ class Main extends React.Component {
           }
           {this.props.displayNarrative || this.props.showOnlyPanels ? null : <Info width={calcUsableWidth(availableWidth, 1)} />}
           {this.props.panelsToDisplay.includes("tree") ? <Tree width={big.width} height={big.height} /> : null}
-          {this.props.panelsToDisplay.includes("map") ? <Map width={big.width} height={big.height} justGotNewDatasetRenderNewMap={false} /> : null}
+          {this.props.panelsToDisplay.includes("map") ? <Map width={big.width} height={big.height} justGotNewDatasetRenderNewMap={false} legend={this.shouldShowMapLegend()} /> : null}
           {this.props.panelsToDisplay.includes("entropy") ?
             (<Suspense fallback={null}>
               <Entropy width={chart.width} height={chart.height} />
diff --git a/src/components/map/map.js b/src/components/map/map.js
index 65614005e..3334ad61d 100644
--- a/src/components/map/map.js
+++ b/src/components/map/map.js
@@ -20,6 +20,8 @@ import { MAP_ANIMATION_PLAY_PAUSE_BUTTON } from "../../actions/types";
 // import { incommingMapPNG } from "../download/helperFunctions";
 import { timerStart, timerEnd } from "../../util/perf";
 import { tabSingle, darkGrey, lightGrey, goColor, pauseColor } from "../../globalStyles";
+import ErrorBoundary from "../../util/errorBoundry";
+import Legend from "../tree/legend/legend";
 
 /* global L */
 // L is global in scope and placed by leaflet()
@@ -640,6 +642,9 @@ class Map extends React.Component {
     // clear layers - store all markers in map state https://github.com/Leaflet/Leaflet/issues/3238#issuecomment-77061011
     return (
       <Card center title={transmissionsExist ? "Transmissions" : "Geography"}>
+        {this.props.legend && <ErrorBoundary>
+          <Legend right width={this.props.width} for="map" />
+        </ErrorBoundary>}
         {this.maybeCreateMapDiv()}
         {this.props.narrativeMode ? null : (
           <button
diff --git a/src/components/tree/legend/legend.js b/src/components/tree/legend/legend.js
index 398f2bcff..0075a3c8a 100644
--- a/src/components/tree/legend/legend.js
+++ b/src/components/tree/legend/legend.js
@@ -8,13 +8,20 @@ import { numericToCalendar } from "../../../util/dateHelpers";
 import { isColorByGenotype, decodeColorByGenotype } from "../../../util/getGenotype";
 import { TOGGLE_LEGEND } from "../../../actions/types";
 
+const svg = {
+  position: "absolute",
+  top: 26,
+  borderRadius: 4,
+  zIndex: 1000,
+  userSelect: "none"
+};
 
-@connect((state) => {
+@connect((state, props) => {
   return {
     colorBy: state.controls.colorBy,
     colorings: state.metadata.colorings,
     colorScale: state.controls.colorScale,
-    legendOpen: state.controls.legendOpen
+    legendOpen: props.for === "tree" ? state.controls.treeLegendOpen : state.controls.mapLegendOpen
   };
 })
 class Legend extends React.Component {
@@ -69,11 +76,16 @@ class Legend extends React.Component {
     return this.props.colorings[this.props.colorBy] === undefined ?
       "" : this.props.colorings[this.props.colorBy].title;
   }
+
   getTitleWidth() {
+    // This is a hack because we can't use getBBox in React.
+    // Lots of work to get measured width of DOM element.
+    // Works fine, but will need adjusting if title font is changed.
     return 15 + 5.3 * this.getTitleString().length;
   }
+
   toggleLegend() {
-    this.props.dispatch({type: TOGGLE_LEGEND, value: !this.props.legendOpen})
+    this.props.dispatch({type: TOGGLE_LEGEND, value: !this.props.legendOpen, for: this.props.for || "tree"});
   }
 
   /*
@@ -85,7 +97,7 @@ class Legend extends React.Component {
       <g id="Title">
         <rect width={this.getTitleWidth()} height="12" fill="rgba(255,255,255,.85)"/>
         <text
-          x={5}
+          x={this.getTitleOffset()}
           y={10}
           style={{
             fontSize: 12,
@@ -106,10 +118,8 @@ class Legend extends React.Component {
    */
   legendChevron() {
     const degrees = this.showLegend() ? -180 : 0;
-    // This is a hack because we can't use getBBox in React.
-    // Lots of work to get measured width of DOM element.
-    // Works fine, but will need adjusting if title font is changed.
-    const offset = this.getTitleWidth();
+
+    const offset = this.getArrowOffset();
     return (
       <g id="Chevron" transform={`translate(${offset},0)`}>
         <svg width="12" height="12" viewBox="0 0 1792 1792">
@@ -187,32 +197,53 @@ class Legend extends React.Component {
 
   getStyles() {
     return {
-      svg: {
-        position: "absolute",
-        left: 5,
-        top: 26,
-        borderRadius: 4,
-        zIndex: 1000,
-        userSelect: "none"
+      svgLeft: {
+        ...svg,
+        left: 5
+      },
+      svgRight: {
+        ...svg,
+        right: 5
       }
     };
   }
+
+  getSVGStyle() {
+    const styles = this.getStyles();
+
+    if (this.props.right) { return styles.svgRight; }
+    return styles.svgLeft;
+  }
+
+  getArrowOffset() {
+    if (this.props.right) {
+      return this.getSVGWidth() - 20;
+    }
+    return this.getTitleWidth();
+  }
+
+  getTitleOffset() {
+    if (this.props.right) {
+      return this.getSVGWidth() - this.getTitleWidth() - 15;
+    }
+    return 5;
+  }
+
   render() {
     // catch the case where we try to render before anythings ready
     if (!this.props.colorScale) return null;
-    const styles = this.getStyles();
     return (
       <svg
         id="TreeLegendContainer"
         width={this.getSVGWidth()}
         height={this.getSVGHeight()}
-        style={styles.svg}
+        style={this.getSVGStyle()}
       >
         {this.legendItems()}
         <g
           id="TitleAndChevron"
           onClick={() => this.toggleLegend()}
-          style={{cursor: "pointer"}}
+          style={{cursor: "pointer", textAlign: "right" }}
         >
           {this.legendTitle()}
           {this.legendChevron()}
diff --git a/src/components/tree/tree.js b/src/components/tree/tree.js
index 284452107..bf94a1c6e 100644
--- a/src/components/tree/tree.js
+++ b/src/components/tree/tree.js
@@ -94,8 +94,8 @@ class Tree extends React.Component {
   }
 
   getStyles = () => {
-    const activeResetTreeButton = this.props.tree.idxOfInViewRootNode !== 0
-      || this.props.treeToo.idxOfInViewRootNode !== 0;
+    const activeResetTreeButton = this.props.tree.idxOfInViewRootNode !== 0 ||
+      this.props.treeToo.idxOfInViewRootNode !== 0;
     return {
       resetTreeButton: {
         zIndex: 100,
@@ -126,7 +126,7 @@ class Tree extends React.Component {
     return (
       <Card center title={"Phylogeny"}>
         <ErrorBoundary>
-          <Legend width={this.props.width}/>
+          <Legend width={this.props.width} for="tree"/>
         </ErrorBoundary>
         <HoverInfoPanel
           hovered={this.state.hovered}
diff --git a/src/reducers/controls.js b/src/reducers/controls.js
index aaff53231..dadcbd019 100644
--- a/src/reducers/controls.js
+++ b/src/reducers/controls.js
@@ -79,7 +79,8 @@ export const getDefaultControlsState = () => {
     zoomMax: undefined,
     branchLengthsToDisplay: "divAndDate",
     sidebarOpen: initialSidebarState.sidebarOpen,
-    legendOpen: undefined,
+    treeLegendOpen: undefined,
+    mapLegendOpen: undefined,
     showOnlyPanels: false
   };
 };
@@ -252,7 +253,10 @@ const Controls = (state = getDefaultControlsState(), action) => {
     case types.TOGGLE_SIDEBAR:
       return Object.assign({}, state, {sidebarOpen: action.value});
     case types.TOGGLE_LEGEND:
-      return Object.assign({}, state, {legendOpen: action.value});
+      if (action.for === 'tree') {
+        return Object.assign({}, state, {treeLegendOpen: action.value});
+      }
+      return Object.assign({}, state, {mapLegendOpen: action.value});
     case types.ADD_COLOR_BYS:
       for (const colorBy of Object.keys(action.newColorings)) {
         state.coloringsPresentOnTree.add(colorBy);

From 099b625a9ebf28b9cddf24937f3a1c37b7107995 Mon Sep 17 00:00:00 2001
From: Cameron Yick <cameron.yick@datadoghq.com>
Date: Thu, 5 Mar 2020 02:17:45 -0500
Subject: [PATCH 02/30] [feature] Improve smoothness of animation for
 temporalWindow movement

---
 src/components/tree/phyloTree/grid.js | 49 +++++++++++++++++++--------
 src/util/globals.js                   | 21 ++++++------
 2 files changed, 45 insertions(+), 25 deletions(-)

diff --git a/src/components/tree/phyloTree/grid.js b/src/components/tree/phyloTree/grid.js
index cb93c36dc..a5c0aabfe 100644
--- a/src/components/tree/phyloTree/grid.js
+++ b/src/components/tree/phyloTree/grid.js
@@ -1,7 +1,9 @@
 /* eslint-disable space-infix-ops */
 import { min, max } from "d3-array";
+import { transition } from "d3-transition";
+import { easeLinear } from "d3-ease";
 import { timerStart, timerEnd } from "../../../util/perf";
-import { months } from "../../../util/globals";
+import { months, animationInterpolationDuration } from "../../../util/globals";
 import { numericToCalendar } from "../../../util/dateHelpers";
 
 export const hideGrid = function hideGrid() {
@@ -19,6 +21,12 @@ export const hideGrid = function hideGrid() {
 const addSVGGroupsIfNeeded = (groups, svg) => {
   if (!("temporalWindow" in groups)) {
     groups.temporalWindow = svg.append("g").attr("id", "temporalWindow");
+
+    // Technically rects aren't groups, but store them to avoid searching for them on each "addTemporalSlice" render.
+    groups.temporalWindowStart = groups.temporalWindow.append('rect')
+      .attr('class', 'temporalWindowStart');
+    groups.temporalWindowEnd = groups.temporalWindow.append('rect')
+      .attr('class', 'temporalWindowEnd');
   }
   if (!("majorGrid" in groups)) {
     groups.majorGrid = svg.append("g").attr("id", "majorGrid");
@@ -334,17 +342,24 @@ export const addGrid = function addGrid() {
   timerEnd("addGrid");
 };
 
-
 export const removeTemporalSlice = function removeTemporalSlice() {
   this.groups.temporalWindow.selectAll("*").remove();
 };
 
+// d3-transition to ensure both rectangles move at the same rate
+export const temporalWindowTransition = transition('temporalWindowTransition')
+  .duration(animationInterpolationDuration)
+  .ease(easeLinear); // the underlying animation uses linear interpolation, let's override the default easeCubic
+
 /**
  * add background grey rectangles to demarcate the temporal slice
  */
 export const addTemporalSlice = function addTemporalSlice() {
-  this.removeTemporalSlice();
-  if (this.layout !== "rect" || this.distance !== "num_date") return;
+  if (this.layout !== "rect" || this.distance !== "num_date") {
+    this.groups.temporalWindow.style('visibility', 'hidden');
+    return;
+  }
+  this.groups.temporalWindow.style('visibility', 'visible');
 
   const xWindow = [this.xScale(this.dateRange[0]), this.xScale(this.dateRange[1])];
   const height = this.yScale.range()[1];
@@ -357,25 +372,29 @@ export const addTemporalSlice = function addTemporalSlice() {
 
   /* the gray region between the root (ish) and the minimum date */
   if (Math.abs(xWindow[0]-rootXPos) > minPxThreshold) { /* don't render anything less than this num of px */
-    this.groups.temporalWindow.append("rect")
-      .attr("x", rightHandTree ? xWindow[0] : 0)
-      .attr("width", rightHandTree ? totalWidth-xWindow[0]: xWindow[0])
-      .attr("y", 0)
+    const xEnd_start = rightHandTree ? totalWidth - xWindow[0] : xWindow[0]; // ending X coordinate of the "start" rectangle
+    const translateX_start = -totalWidth + xEnd_start; // translation distance for starting temporalWindow
+    this.groups.temporalWindowStart
       .attr("height", height)
-      .attr("fill", fill);
+      .attr("width", totalWidth)
+      .attr("fill", fill)
+      .transition('temporalWindowTransition')
+      .attr("transform", `translate(${translateX_start},0)`);
   }
 
   /* the gray region between the maximum selected date and the last tip */
-  const startingX = rightHandTree ? this.params.margins.right : xWindow[1];
+  const xStart_end = rightHandTree ? this.params.margins.right : xWindow[1]; // starting X coordinate of the "end" rectangle
   const rectWidth = rightHandTree ?
     xWindow[1]-this.params.margins.right :
     totalWidth-this.params.margins.right-xWindow[1];
+  const translateX_end = xStart_end + this.params.margins.left;
+
   if (rectWidth > minPxThreshold) {
-    this.groups.temporalWindow.append("rect")
-      .attr("x", startingX)
-      .attr("width", rectWidth)
-      .attr("y", 0)
+    this.groups.temporalWindowEnd
       .attr("height", height)
-      .attr("fill", fill);
+      .attr("width", totalWidth)
+      .attr("fill", fill)
+      .transition('temporalWindowTransition')
+      .attr("transform", `translate(${translateX_end},0)`);
   }
 };
diff --git a/src/util/globals.js b/src/util/globals.js
index 413cdbf35..2f86231e9 100644
--- a/src/util/globals.js
+++ b/src/util/globals.js
@@ -2,13 +2,13 @@ import { scaleLinear, scaleSqrt } from "d3-scale";
 import { hasExtension, getExtension } from "../util/extensions";
 
 export const colorOptions = {
-  "country": {"key": "country", "legendTitle": "Country", "menuItem": "country", "type": "discrete"},
-  "region": {"key": "region", "legendTitle": "Region", "menuItem": "region", "type": "discrete"},
-  "num_date": {"key": "num_date", "legendTitle": "Sampling date", "menuItem": "date", "type": "continuous"},
-  "ep": {"key": "ep", "legendTitle": "Epitope Mutations", "menuItem": "epitope mutations", "type": "continuous"},
-  "ne": {"key": "ne", "legendTitle": "Non-epitope Mutations", "menuItem": "nonepitope mutations", "type": "continuous"},
-  "rb": {"key": "rb", "legendTitle": "Receptor Binding Mutations", "menuItem": "RBS mutations", "type": "continuous"},
-  "gt": {"key": "genotype", "legendTitle": "Genotype", "menuItem": "genotype", "type": "discrete"}
+  country: {key: "country", legendTitle: "Country", menuItem: "country", type: "discrete"},
+  region: {key: "region", legendTitle: "Region", menuItem: "region", type: "discrete"},
+  num_date: {key: "num_date", legendTitle: "Sampling date", menuItem: "date", type: "continuous"},
+  ep: {key: "ep", legendTitle: "Epitope Mutations", menuItem: "epitope mutations", type: "continuous"},
+  ne: {key: "ne", legendTitle: "Non-epitope Mutations", menuItem: "nonepitope mutations", type: "continuous"},
+  rb: {key: "rb", legendTitle: "Receptor Binding Mutations", menuItem: "RBS mutations", type: "continuous"},
+  gt: {key: "genotype", legendTitle: "Genotype", menuItem: "genotype", type: "discrete"}
 };
 
 /* static for now, then hand rolled version of https://github.com/digidem/react-dimensions */
@@ -29,7 +29,7 @@ export const defaultDistanceMeasure = "num_date";
 export const defaultDateRange = 6;
 export const date_select = true;
 export const file_prefix = "Zika_";
-export const restrictTo = {"region": "all"};
+export const restrictTo = {region: "all"};
 export const time_window = 3.0;
 export const fullDataTimeWindow = 1.5;
 export const time_ticks = [2013.0, 2013.5, 2014.0, 2014.5, 2015.0, 2015.5, 2016.0];
@@ -63,6 +63,7 @@ export const slowTransitionDuration = 1400; // in milliseconds
 export const animationWindowWidth = 0.075; // width of animation window relative to date slider
 export const minDistanceDateSlider = 0.075;
 export const animationTick = 50; // animation tick in milliseconds
+export const animationInterpolationDuration = 10; // how long d3 temporalWindow transitions last in milliseconds. Must be shorter than animationTick.
 export const HIColorDomain = genericDomain.map((d) => {
   return Math.round(100 * (d * 3.6)) / 100;
 });
@@ -130,8 +131,8 @@ export const colors = [
   ["#511EA8", "#4928B4", "#4334BF", "#4041C7", "#3F50CC", "#3F5ED0", "#416CCE", "#4379CD", "#4784C7", "#4B8FC1", "#5098B9", "#56A0AF", "#5CA7A4", "#63AC99", "#6BB18E", "#73B583", "#7CB878", "#86BB6E", "#90BC65", "#9ABD5C", "#A4BE56", "#AFBD4F", "#B9BC4A", "#C2BA46", "#CCB742", "#D3B240", "#DAAC3D", "#DFA43B", "#E39B39", "#E68F36", "#E68234", "#E67431", "#E4632E", "#E1512A", "#DF4027", "#DC2F24"]
 ];
 
-export const filterAbbrFwd = {"geo": "geographic location", "all": "all"};
-export const filterAbbrRev = {"geographic location": "geo", "all": "all"};
+export const filterAbbrFwd = {geo: "geographic location", all: "all"};
+export const filterAbbrRev = {"geographic location": "geo", all: "all"};
 
 export const titleColors = ["#4377CD", "#5097BA", "#63AC9A", "#7CB879", "#9ABE5C", "#B9BC4A", "#D4B13F", "#E49938", "#E67030", "#DE3C26"];
 export const notificationDuration = 10000;

From 6ea60d070143108d0f0ddf8ecf87746a3c034dc0 Mon Sep 17 00:00:00 2001
From: Cameron Yick <cameron.yick@datadoghq.com>
Date: Tue, 10 Mar 2020 20:57:28 -0400
Subject: [PATCH 03/30] [feature] Adapt transition-based animation to work with
 rightHandTree coordinate system

---
 src/components/tree/phyloTree/grid.js | 38 +++++++++++++++++++--------
 1 file changed, 27 insertions(+), 11 deletions(-)

diff --git a/src/components/tree/phyloTree/grid.js b/src/components/tree/phyloTree/grid.js
index a5c0aabfe..227604ee5 100644
--- a/src/components/tree/phyloTree/grid.js
+++ b/src/components/tree/phyloTree/grid.js
@@ -372,29 +372,45 @@ export const addTemporalSlice = function addTemporalSlice() {
 
   /* the gray region between the root (ish) and the minimum date */
   if (Math.abs(xWindow[0]-rootXPos) > minPxThreshold) { /* don't render anything less than this num of px */
-    const xEnd_start = rightHandTree ? totalWidth - xWindow[0] : xWindow[0]; // ending X coordinate of the "start" rectangle
-    const translateX_start = -totalWidth + xEnd_start; // translation distance for starting temporalWindow
+    let xEnd_startRegion = xWindow[0]; // ending X coordinate of the "start" rectangle
+    let translateX_startRegion = -totalWidth + xEnd_startRegion; // translation distance for the start rectangle
+
+    // With right hand tree, the coordinate system flips (right to left)
+    if (rightHandTree) {
+      xEnd_startRegion = totalWidth - xWindow[0];
+      translateX_startRegion = xWindow[0];
+    }
+
     this.groups.temporalWindowStart
       .attr("height", height)
       .attr("width", totalWidth)
       .attr("fill", fill)
       .transition('temporalWindowTransition')
-      .attr("transform", `translate(${translateX_start},0)`);
+      .attr("transform", `translate(${translateX_startRegion},0)`);
   }
 
   /* the gray region between the maximum selected date and the last tip */
-  const xStart_end = rightHandTree ? this.params.margins.right : xWindow[1]; // starting X coordinate of the "end" rectangle
-  const rectWidth = rightHandTree ?
-    xWindow[1]-this.params.margins.right :
-    totalWidth-this.params.margins.right-xWindow[1];
-  const translateX_end = xStart_end + this.params.margins.left;
+  let xStart_endRegion = xWindow[1]; // starting X coordinate of the "end" rectangle
+  let width_endRegion = totalWidth - this.params.margins.right - xWindow[1];
 
-  if (rectWidth > minPxThreshold) {
+  // With a right hand tree, the coordinate system flips (right to left)
+  if (rightHandTree) {
+    xStart_endRegion = this.params.margins.right;
+    width_endRegion = xWindow[1] - this.params.margins.right;
+  }
+
+  if (width_endRegion > minPxThreshold) {
     this.groups.temporalWindowEnd
+      .attr('visibility', 'visible')
       .attr("height", height)
-      .attr("width", totalWidth)
       .attr("fill", fill)
       .transition('temporalWindowTransition')
-      .attr("transform", `translate(${translateX_end},0)`);
+      .attr("transform", `translate(${xStart_endRegion},0)`)
+      // Unlike the startingRegion, this panel cannot depend
+    // on letting the SVG boundaries clip part of the rectangle.
+    // As a result, we'll have to animate width AND height.
+      .attr("width", width_endRegion);
+  } else {
+    this.groups.temporalWindowEnd.attr('visibility', 'hidden');
   }
 };

From 2c0752ee22a1d8709fe5153fe30cc9d528d85c58 Mon Sep 17 00:00:00 2001
From: Cameron Yick <cameron.yick@datadoghq.com>
Date: Tue, 10 Mar 2020 21:10:57 -0400
Subject: [PATCH 04/30] [animation] Clarify names for show/hiding temporal
 slices

---
 src/components/tree/phyloTree/change.js    |  9 +++++----
 src/components/tree/phyloTree/grid.js      | 13 ++++++++-----
 src/components/tree/phyloTree/phyloTree.js |  4 ++--
 src/components/tree/phyloTree/renderers.js |  2 +-
 4 files changed, 16 insertions(+), 12 deletions(-)

diff --git a/src/components/tree/phyloTree/change.js b/src/components/tree/phyloTree/change.js
index e4b355a94..0bd7f7232 100644
--- a/src/components/tree/phyloTree/change.js
+++ b/src/components/tree/phyloTree/change.js
@@ -179,7 +179,7 @@ export const modifySVG = function modifySVG(elemsToUpdate, svgPropsToUpdate, tra
 
   /* background temporal time slice */
   if (extras.timeSliceHasPotentiallyChanged) {
-    this.addTemporalSlice();
+    this.showTemporalSlice();
   }
 
   /* branch labels */
@@ -208,7 +208,7 @@ export const modifySVGInStages = function modifySVGInStages(elemsToUpdate, svgPr
     this.drawTips();
     this.updateTipLabels();
     if (this.vaccines) this.drawVaccines();
-    this.addTemporalSlice();
+    this.showTemporalSlice();
     if (this.layout === "clock" && this.distance === "num_date") this.drawRegression();
     if (elemsToUpdate.has(".branchLabel")) this.drawBranchLabels(this.params.branchLabelKey);
   };
@@ -230,7 +230,7 @@ export const modifySVGInStages = function modifySVGInStages(elemsToUpdate, svgPr
     .remove()
     .on("start", () => inProgress++)
     .on("end", step2);
-  this.removeTemporalSlice();
+  this.hideTemporalSlice();
   if (!transitionTimeFadeOut) timerFlush();
 };
 
@@ -309,7 +309,8 @@ export const change = function change({
     elemsToUpdate.add(".vaccineCross").add(".vaccineDottedLine").add(".conf");
     elemsToUpdate.add('.branchLabel').add('.tipLabel');
     elemsToUpdate.add(".grid").add(".regression");
-    svgPropsToUpdate.add("cx").add("cy").add("d").add("opacity").add("visibility");
+    svgPropsToUpdate.add("cx").add("cy").add("d").add("opacity")
+.add("visibility");
   }
 
   /* change the requested properties on the nodes */
diff --git a/src/components/tree/phyloTree/grid.js b/src/components/tree/phyloTree/grid.js
index 227604ee5..04ef586ce 100644
--- a/src/components/tree/phyloTree/grid.js
+++ b/src/components/tree/phyloTree/grid.js
@@ -22,7 +22,7 @@ const addSVGGroupsIfNeeded = (groups, svg) => {
   if (!("temporalWindow" in groups)) {
     groups.temporalWindow = svg.append("g").attr("id", "temporalWindow");
 
-    // Technically rects aren't groups, but store them to avoid searching for them on each "addTemporalSlice" render.
+    // Technically rects aren't groups, but store them to avoid searching for them on each "showTemporalSlice" render.
     groups.temporalWindowStart = groups.temporalWindow.append('rect')
       .attr('class', 'temporalWindowStart');
     groups.temporalWindowEnd = groups.temporalWindow.append('rect')
@@ -342,8 +342,9 @@ export const addGrid = function addGrid() {
   timerEnd("addGrid");
 };
 
-export const removeTemporalSlice = function removeTemporalSlice() {
-  this.groups.temporalWindow.selectAll("*").remove();
+export const hideTemporalSlice = function hideTemporalSlice() {
+  this.groups.temporalWindowStart.attr('visibility', 'hidden');
+  this.groups.temporalWindowEnd.attr('visibility', 'hidden');
 };
 
 // d3-transition to ensure both rectangles move at the same rate
@@ -354,12 +355,11 @@ export const temporalWindowTransition = transition('temporalWindowTransition')
 /**
  * add background grey rectangles to demarcate the temporal slice
  */
-export const addTemporalSlice = function addTemporalSlice() {
+export const showTemporalSlice = function showTemporalSlice() {
   if (this.layout !== "rect" || this.distance !== "num_date") {
     this.groups.temporalWindow.style('visibility', 'hidden');
     return;
   }
-  this.groups.temporalWindow.style('visibility', 'visible');
 
   const xWindow = [this.xScale(this.dateRange[0]), this.xScale(this.dateRange[1])];
   const height = this.yScale.range()[1];
@@ -382,11 +382,14 @@ export const addTemporalSlice = function addTemporalSlice() {
     }
 
     this.groups.temporalWindowStart
+      .attr('visibility', 'visible')
       .attr("height", height)
       .attr("width", totalWidth)
       .attr("fill", fill)
       .transition('temporalWindowTransition')
       .attr("transform", `translate(${translateX_startRegion},0)`);
+  } else {
+    this.groups.temporalWindowStart.attr('visibility', 'hidden');
   }
 
   /* the gray region between the maximum selected date and the last tip */
diff --git a/src/components/tree/phyloTree/phyloTree.js b/src/components/tree/phyloTree/phyloTree.js
index 8b373a76a..000662884 100644
--- a/src/components/tree/phyloTree/phyloTree.js
+++ b/src/components/tree/phyloTree/phyloTree.js
@@ -89,7 +89,7 @@ PhyloTree.prototype.removeTipLabels = labels.removeTipLabels;
 /* G R I D */
 PhyloTree.prototype.hideGrid = grid.hideGrid;
 PhyloTree.prototype.addGrid = grid.addGrid;
-PhyloTree.prototype.addTemporalSlice = grid.addTemporalSlice;
-PhyloTree.prototype.removeTemporalSlice = grid.removeTemporalSlice;
+PhyloTree.prototype.showTemporalSlice = grid.showTemporalSlice;
+PhyloTree.prototype.hideTemporalSlice = grid.hideTemporalSlice;
 
 export default PhyloTree;
diff --git a/src/components/tree/phyloTree/renderers.js b/src/components/tree/phyloTree/renderers.js
index 18d4c3595..b23bfcea9 100644
--- a/src/components/tree/phyloTree/renderers.js
+++ b/src/components/tree/phyloTree/renderers.js
@@ -43,7 +43,7 @@ export const render = function render(svg, layout, distance, parameters, callbac
   /* draw functions */
   if (this.params.showGrid) {
     this.addGrid();
-    this.addTemporalSlice();
+    this.showTemporalSlice();
   }
   this.drawBranches();
   this.drawTips();

From eb2629f76feca3e3e9390537fdc15fef33ca8598 Mon Sep 17 00:00:00 2001
From: Cameron Yick <cameron.yick@datadoghq.com>
Date: Tue, 10 Mar 2020 21:45:25 -0400
Subject: [PATCH 05/30] [animation] Remove unnecessary animation when frame
 transitions between appearing and disappearing, replace visibility with
 opacity

---
 src/components/tree/phyloTree/grid.js | 55 ++++++++++++++++++---------
 1 file changed, 37 insertions(+), 18 deletions(-)

diff --git a/src/components/tree/phyloTree/grid.js b/src/components/tree/phyloTree/grid.js
index 04ef586ce..929378a30 100644
--- a/src/components/tree/phyloTree/grid.js
+++ b/src/components/tree/phyloTree/grid.js
@@ -343,8 +343,8 @@ export const addGrid = function addGrid() {
 };
 
 export const hideTemporalSlice = function hideTemporalSlice() {
-  this.groups.temporalWindowStart.attr('visibility', 'hidden');
-  this.groups.temporalWindowEnd.attr('visibility', 'hidden');
+  this.groups.temporalWindowStart.attr('opacity', 0);
+  this.groups.temporalWindowEnd.attr('opacity', 0);
 };
 
 // d3-transition to ensure both rectangles move at the same rate
@@ -372,24 +372,33 @@ export const showTemporalSlice = function showTemporalSlice() {
 
   /* the gray region between the root (ish) and the minimum date */
   if (Math.abs(xWindow[0]-rootXPos) > minPxThreshold) { /* don't render anything less than this num of px */
-    let xEnd_startRegion = xWindow[0]; // ending X coordinate of the "start" rectangle
-    let translateX_startRegion = -totalWidth + xEnd_startRegion; // translation distance for the start rectangle
+    let width_startRegion = xWindow[0];
+    let translateX_startRegion = 0;
 
     // With right hand tree, the coordinate system flips (right to left)
     if (rightHandTree) {
-      xEnd_startRegion = totalWidth - xWindow[0];
+      width_startRegion = totalWidth - xWindow[0];
       translateX_startRegion = xWindow[0];
     }
 
+    const wasStartRegionVisible = this.groups.temporalWindowStart.attr('opacity') === 1;
+
     this.groups.temporalWindowStart
-      .attr('visibility', 'visible')
+      .attr('opacity', 1)
       .attr("height", height)
-      .attr("width", totalWidth)
-      .attr("fill", fill)
-      .transition('temporalWindowTransition')
-      .attr("transform", `translate(${translateX_startRegion},0)`);
+      .attr("transform", `translate(${translateX_startRegion},0)`)
+      .attr("fill", fill);
+
+    // Only apply animation if rectangle was already visible in the previous frame.
+    if (wasStartRegionVisible) {
+      this.groups.temporalWindowStart.transition('temporalWindowTransition')
+        .attr("width", width_startRegion);
+    } else {
+      this.groups.temporalWindowStart
+        .attr("width", width_startRegion);
+    }
   } else {
-    this.groups.temporalWindowStart.attr('visibility', 'hidden');
+    this.groups.temporalWindowStart.attr('opacity', 0);
   }
 
   /* the gray region between the maximum selected date and the last tip */
@@ -403,17 +412,27 @@ export const showTemporalSlice = function showTemporalSlice() {
   }
 
   if (width_endRegion > minPxThreshold) {
+    const wasEndRegionVisible = this.groups.temporalWindowEnd.attr('opacity') === 1;
+
     this.groups.temporalWindowEnd
-      .attr('visibility', 'visible')
+      .attr('opacity', 1)
       .attr("height", height)
-      .attr("fill", fill)
-      .transition('temporalWindowTransition')
-      .attr("transform", `translate(${xStart_endRegion},0)`)
-      // Unlike the startingRegion, this panel cannot depend
+      .attr("fill", fill);
+    // Only apply animation if rectangle was already visible in the previous frame.
+    // Unlike the startingRegion, this panel cannot depend
     // on letting the SVG boundaries clip part of the rectangle.
     // As a result, we'll have to animate width AND height.
-      .attr("width", width_endRegion);
+    if (wasEndRegionVisible) {
+      this.groups.temporalWindowEnd
+        .transition('temporalWindowTransition')
+        .attr("transform", `translate(${xStart_endRegion},0)`)
+        .attr("width", width_endRegion);
+    } else {
+      this.groups.temporalWindowEnd
+        .attr("transform", `translate(${xStart_endRegion},0)`)
+        .attr("width", width_endRegion);
+    }
   } else {
-    this.groups.temporalWindowEnd.attr('visibility', 'hidden');
+    this.groups.temporalWindowEnd.attr('opacity', 0);
   }
 };

From 27bbba173836bf955ebcf6d15fa63f7b0ac1c798 Mon Sep 17 00:00:00 2001
From: Cameron Yick <cameron.yick@datadoghq.com>
Date: Tue, 10 Mar 2020 23:21:47 -0400
Subject: [PATCH 06/30] Polish jumpy-ness in the endRegion animation by using
 CSS scaling

---
 src/components/tree/phyloTree/change.js |  3 +--
 src/components/tree/phyloTree/grid.js   | 19 ++++++++++++-------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/components/tree/phyloTree/change.js b/src/components/tree/phyloTree/change.js
index 0bd7f7232..9e3253e2a 100644
--- a/src/components/tree/phyloTree/change.js
+++ b/src/components/tree/phyloTree/change.js
@@ -309,8 +309,7 @@ export const change = function change({
     elemsToUpdate.add(".vaccineCross").add(".vaccineDottedLine").add(".conf");
     elemsToUpdate.add('.branchLabel').add('.tipLabel');
     elemsToUpdate.add(".grid").add(".regression");
-    svgPropsToUpdate.add("cx").add("cy").add("d").add("opacity")
-.add("visibility");
+    svgPropsToUpdate.add("cx").add("cy").add("d").add("opacity").add("visibility");
   }
 
   /* change the requested properties on the nodes */
diff --git a/src/components/tree/phyloTree/grid.js b/src/components/tree/phyloTree/grid.js
index 929378a30..8521ca65f 100644
--- a/src/components/tree/phyloTree/grid.js
+++ b/src/components/tree/phyloTree/grid.js
@@ -357,7 +357,7 @@ export const temporalWindowTransition = transition('temporalWindowTransition')
  */
 export const showTemporalSlice = function showTemporalSlice() {
   if (this.layout !== "rect" || this.distance !== "num_date") {
-    this.groups.temporalWindow.style('visibility', 'hidden');
+    this.hideTemporalSlice();
     return;
   }
 
@@ -381,7 +381,7 @@ export const showTemporalSlice = function showTemporalSlice() {
       translateX_startRegion = xWindow[0];
     }
 
-    const wasStartRegionVisible = this.groups.temporalWindowStart.attr('opacity') === 1;
+    const wasStartRegionVisible = this.groups.temporalWindowStart.attr('opacity') === '1';
 
     this.groups.temporalWindowStart
       .attr('opacity', 1)
@@ -405,31 +405,36 @@ export const showTemporalSlice = function showTemporalSlice() {
   let xStart_endRegion = xWindow[1]; // starting X coordinate of the "end" rectangle
   let width_endRegion = totalWidth - this.params.margins.right - xWindow[1];
 
+  let transform_endRegion = `translate(${totalWidth - this.params.margins.right},0) scale(-1,1)`;
   // With a right hand tree, the coordinate system flips (right to left)
   if (rightHandTree) {
     xStart_endRegion = this.params.margins.right;
     width_endRegion = xWindow[1] - this.params.margins.right;
+    transform_endRegion = `translate(${xStart_endRegion},0)`;
   }
 
   if (width_endRegion > minPxThreshold) {
-    const wasEndRegionVisible = this.groups.temporalWindowEnd.attr('opacity') === 1;
+    const wasEndRegionVisible = this.groups.temporalWindowEnd.attr('opacity') === '1';
 
     this.groups.temporalWindowEnd
       .attr('opacity', 1)
       .attr("height", height)
-      .attr("fill", fill);
+      .attr("fill", fill)
+      .attr("transform", transform_endRegion);
+
+
     // Only apply animation if rectangle was already visible in the previous frame.
     // Unlike the startingRegion, this panel cannot depend
     // on letting the SVG boundaries clip part of the rectangle.
-    // As a result, we'll have to animate width AND height.
+    // As a result, we'll have to animate width instead of position
+    // If performance becomes an issue, try add a custom clip-path with
+    // a fixed-width region instead.
     if (wasEndRegionVisible) {
       this.groups.temporalWindowEnd
         .transition('temporalWindowTransition')
-        .attr("transform", `translate(${xStart_endRegion},0)`)
         .attr("width", width_endRegion);
     } else {
       this.groups.temporalWindowEnd
-        .attr("transform", `translate(${xStart_endRegion},0)`)
         .attr("width", width_endRegion);
     }
   } else {

From 14133ba06539f4f24aaccdd7fcb8a07a349d3796 Mon Sep 17 00:00:00 2001
From: Cameron Devine <camerondtrain@gmail.com>
Date: Tue, 17 Mar 2020 00:13:16 -0700
Subject: [PATCH 07/30] allowing scrolling in narrative sidebar

---
 src/components/narrative/ReactPageScroller.js | 56 ++++++++++---------
 src/components/narrative/index.js             |  3 +-
 2 files changed, 33 insertions(+), 26 deletions(-)

diff --git a/src/components/narrative/ReactPageScroller.js b/src/components/narrative/ReactPageScroller.js
index 61b2a76f4..5a21d0a70 100644
--- a/src/components/narrative/ReactPageScroller.js
+++ b/src/components/narrative/ReactPageScroller.js
@@ -105,20 +105,23 @@ export default class ReactPageScroller extends React.Component {
         this[scrollWindowUp] = () => {
             if (!_.isNil(this["container_" + (this.state.componentIndex - 1)]) && !this[scrolling]) {
 
-                this[scrolling] = true;
-                this._pageContainer.style.transform = `translate3d(0, ${(this.state.componentIndex - 1) * -100}%, 0)`;
-
-                if (this.props.pageOnChange) {
-                    this.props.pageOnChange(this.state.componentIndex);
+                var element = this["container_" + this.state.componentIndex].getElementsByTagName('div')[0];
+                if (element.scrollTop === 0) {
+                  this[scrolling] = true;
+                  this._pageContainer.style.transform = `translate3d(0, ${(this.state.componentIndex - 1) * -100}%, 0)`;
+
+                  if (this.props.pageOnChange) {
+                      this.props.pageOnChange(this.state.componentIndex);
+                  }
+
+                  setTimeout(() => {
+                      this.setState((prevState) => ({componentIndex: prevState.componentIndex - 1}), () => {
+                          this[scrolling] = false;
+                          this[previousTouchMove] = null;
+                      });
+                  }, this.props.animationTimer + ANIMATION_TIMER)
                 }
 
-                setTimeout(() => {
-                    this.setState((prevState) => ({componentIndex: prevState.componentIndex - 1}), () => {
-                        this[scrolling] = false;
-                        this[previousTouchMove] = null;
-                    });
-                }, this.props.animationTimer + ANIMATION_TIMER)
-
             } else if (this.props.scrollUnavailable) {
                 this.props.scrollUnavailable();
             }
@@ -127,21 +130,24 @@ export default class ReactPageScroller extends React.Component {
         this[scrollWindowDown] = () => {
             if (!_.isNil(this["container_" + (this.state.componentIndex + 1)]) && !this[scrolling]) {
 
-                this[scrolling] = true;
-                this._pageContainer.style.transform = `translate3d(0, ${(this.state.componentIndex + 1) * -100}%, 0)`;
-
-                if (this.props.pageOnChange) {
-                    this.props.pageOnChange(this.state.componentIndex + 2);
+                var element = this["container_" + this.state.componentIndex].getElementsByTagName('div')[0];
+                if (element.scrollTop === element.scrollHeight - element.clientHeight) {
+                  this[scrolling] = true;
+                  this._pageContainer.style.transform = `translate3d(0, ${(this.state.componentIndex + 1) * -100}%, 0)`;
+
+                  if (this.props.pageOnChange) {
+                      this.props.pageOnChange(this.state.componentIndex + 2);
+                  }
+
+                  setTimeout(() => {
+                      this.setState((prevState) => ({componentIndex: prevState.componentIndex + 1}), () => {
+                          this[scrolling] = false;
+                          this[previousTouchMove] = null;
+                          this[addNextComponent]();
+                      });
+                  }, this.props.animationTimer + ANIMATION_TIMER)
                 }
 
-                setTimeout(() => {
-                    this.setState((prevState) => ({componentIndex: prevState.componentIndex + 1}), () => {
-                        this[scrolling] = false;
-                        this[previousTouchMove] = null;
-                        this[addNextComponent]();
-                    });
-                }, this.props.animationTimer + ANIMATION_TIMER)
-
             } else if (this.props.scrollUnavailable) {
                 this.props.scrollUnavailable();
             }
diff --git a/src/components/narrative/index.js b/src/components/narrative/index.js
index 5699b677b..406159fee 100644
--- a/src/components/narrative/index.js
+++ b/src/components/narrative/index.js
@@ -151,7 +151,8 @@ class Narrative extends React.Component {
           style={{
             padding: "10px 20px",
             height: "inherit",
-            overflow: "hidden"
+            overflowX: "hidden",
+            overflowY: "auto"
           }}
           dangerouslySetInnerHTML={{__html}}
         />

From a4ea5fe8bed7f7f3d2145208f012ecca52028eb6 Mon Sep 17 00:00:00 2001
From: Cameron Devine <camerondtrain@gmail.com>
Date: Tue, 17 Mar 2020 00:34:24 -0700
Subject: [PATCH 08/30] only changing narrative page when a large enough scroll
 value is present

---
 src/components/narrative/ReactPageScroller.js | 21 ++++++++++---------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/src/components/narrative/ReactPageScroller.js b/src/components/narrative/ReactPageScroller.js
index 5a21d0a70..6cdd48a68 100644
--- a/src/components/narrative/ReactPageScroller.js
+++ b/src/components/narrative/ReactPageScroller.js
@@ -20,6 +20,7 @@ const scrollWindowDown = Symbol();
 const ANIMATION_TIMER = 200;
 const KEY_UP = 38;
 const KEY_DOWN = 40;
+const SCROLL_THRESHOLD = 25;
 
 export default class ReactPageScroller extends React.Component {
     static propTypes = {
@@ -47,9 +48,9 @@ export default class ReactPageScroller extends React.Component {
 
         this[wheelScroll] = (event) => {
             if (event.deltaY < 0) {
-                this[scrollWindowUp]();
+                this[scrollWindowUp](-event.deltaY);
             } else {
-                this[scrollWindowDown]();
+                this[scrollWindowDown](event.deltaY);
             }
 
         };
@@ -57,9 +58,9 @@ export default class ReactPageScroller extends React.Component {
         this[touchMove] = (event) => {
             if (!_.isNull(this[previousTouchMove])) {
                 if (event.touches[0].clientY > this[previousTouchMove]) {
-                    this[scrollWindowUp]();
+                    this[scrollWindowUp](SCROLL_THRESHOLD);
                 } else {
-                    this[scrollWindowDown]();
+                    this[scrollWindowDown](SCROLL_THRESHOLD);
                 }
             } else {
                 this[previousTouchMove] = event.touches[0].clientY;
@@ -68,10 +69,10 @@ export default class ReactPageScroller extends React.Component {
 
         this[keyPress] = (event) => {
             if (_.isEqual(event.keyCode, KEY_UP)) {
-                this[scrollWindowUp]();
+                this[scrollWindowUp](SCROLL_THRESHOLD);
             }
             if (_.isEqual(event.keyCode, KEY_DOWN)) {
-                this[scrollWindowDown]();
+                this[scrollWindowDown](SCROLL_THRESHOLD);
             }
         };
 
@@ -102,11 +103,11 @@ export default class ReactPageScroller extends React.Component {
             this.setState({componentsToRender: [...componentsToRender]});
         };
 
-        this[scrollWindowUp] = () => {
+        this[scrollWindowUp] = (amount) => {
             if (!_.isNil(this["container_" + (this.state.componentIndex - 1)]) && !this[scrolling]) {
 
                 var element = this["container_" + this.state.componentIndex].getElementsByTagName('div')[0];
-                if (element.scrollTop === 0) {
+                if (element.scrollTop === 0 && amount >= SCROLL_THRESHOLD) {
                   this[scrolling] = true;
                   this._pageContainer.style.transform = `translate3d(0, ${(this.state.componentIndex - 1) * -100}%, 0)`;
 
@@ -127,11 +128,11 @@ export default class ReactPageScroller extends React.Component {
             }
         };
 
-        this[scrollWindowDown] = () => {
+        this[scrollWindowDown] = (amount) => {
             if (!_.isNil(this["container_" + (this.state.componentIndex + 1)]) && !this[scrolling]) {
 
                 var element = this["container_" + this.state.componentIndex].getElementsByTagName('div')[0];
-                if (element.scrollTop === element.scrollHeight - element.clientHeight) {
+                if (element.scrollTop === element.scrollHeight - element.clientHeight && amount >= SCROLL_THRESHOLD) {
                   this[scrolling] = true;
                   this._pageContainer.style.transform = `translate3d(0, ${(this.state.componentIndex + 1) * -100}%, 0)`;
 

From e8eb38827b3b3120cb1de7423ecd1009fd080541 Mon Sep 17 00:00:00 2001
From: Cameron Devine <camerondtrain@gmail.com>
Date: Fri, 27 Mar 2020 12:26:45 -0700
Subject: [PATCH 09/30] reduced the hight of the left hand scolled pages and
 added some padding to correctly fit the content.

---
 src/components/narrative/ReactPageScroller.js | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/components/narrative/ReactPageScroller.js b/src/components/narrative/ReactPageScroller.js
index 6cdd48a68..5f8d7f1e1 100644
--- a/src/components/narrative/ReactPageScroller.js
+++ b/src/components/narrative/ReactPageScroller.js
@@ -172,7 +172,7 @@ export default class ReactPageScroller extends React.Component {
           <div
             key={this.state.componentIndex}
             ref={c => this["container_" + this.state.componentIndex] = c}
-            style={{height: "100%", width: "100%"}}
+            style={{height: "calc(100% - 20px)", width: "100%", "padding-bottom": "20px"}}
           >
             {this.props.children[this.state.componentIndex]}
           </div>
@@ -181,7 +181,7 @@ export default class ReactPageScroller extends React.Component {
         componentsToRender.push(
           <div
             ref={c => this["container_" + this.state.componentIndex] = c}
-            style={{height: "100%", width: "100%"}}
+            style={{height: "calc(100% - 20px)", width: "100%", "padding-bottom": "20px"}}
           >
             {this.props.children}
           </div>
@@ -224,7 +224,7 @@ export default class ReactPageScroller extends React.Component {
                 componentsToRender.push(
                     <div key={number + 1}
                             ref={c => this["container_" + (number + 1)] = c}
-                            style={{height: "100%", width: "100%"}}>
+                            style={{height: "calc(100% - 20px)", width: "100%", "padding-bottom": "20px"}}>
                         {children[number + 1]}
                     </div>
                 );
@@ -244,7 +244,7 @@ export default class ReactPageScroller extends React.Component {
                 componentsToRender.push(
                     <div key={i}
                             ref={c => this["container_" + i] = c}
-                            style={{height: "100%", width: "100%"}}>
+                            style={{height: "calc(100% - 20px)", width: "100%", "padding-bottom": "20px"}}>
                         {children[i]}
                     </div>
                 );
@@ -254,7 +254,7 @@ export default class ReactPageScroller extends React.Component {
                 componentsToRender.push(
                     <div key={number + 1}
                             ref={c => this["container_" + (number + 1)] = c}
-                            style={{height: "100%", width: "100%"}}>
+                            style={{height: "calc(100% - 20px)", width: "100%", "padding-bottom": "20px"}}>
                         {children[number + 1]}
                     </div>
                 );

From 2f9f2ce822060d2dd56f87fd1f28986648ab60a0 Mon Sep 17 00:00:00 2001
From: Avin <avinkavesha@gmail.com>
Date: Sat, 28 Mar 2020 23:32:01 +0530
Subject: [PATCH 10/30] optimize: add babel-lodash-loader

---
 babel.config.js   |  1 +
 package-lock.json | 62 ++++++++++++++++++++++++++++++++++++++---------
 package.json      |  1 +
 3 files changed, 52 insertions(+), 12 deletions(-)

diff --git a/babel.config.js b/babel.config.js
index f269f2f76..9bd2f2f69 100644
--- a/babel.config.js
+++ b/babel.config.js
@@ -18,6 +18,7 @@ module.exports = function babelConfig(api) {
     "babel-plugin-styled-components",
     "babel-plugin-syntax-dynamic-import",
     "@babel/plugin-transform-runtime",
+    "lodash"
   ];
   if (api.env("development")) {
     if (process.env.BABEL_EXTENSION_PATH && !process.env.BABEL_EXTENSION_PATH.includes(__dirname)) {
diff --git a/package-lock.json b/package-lock.json
index 2a6fccd77..36fdd9baf 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "auspice",
-  "version": "2.9.1",
+  "version": "2.11.1",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
@@ -2369,6 +2369,19 @@
         "@types/babel__traverse": "^7.0.6"
       }
     },
+    "babel-plugin-lodash": {
+      "version": "3.3.4",
+      "resolved": "https://registry.npmjs.org/babel-plugin-lodash/-/babel-plugin-lodash-3.3.4.tgz",
+      "integrity": "sha512-yDZLjK7TCkWl1gpBeBGmuaDIFhZKmkoL+Cu2MUUjv5VxUZx/z7tBGBCBcQs5RI1Bkz5LLmNdjx7paOyQtMovyg==",
+      "dev": true,
+      "requires": {
+        "@babel/helper-module-imports": "^7.0.0-beta.49",
+        "@babel/types": "^7.0.0-beta.49",
+        "glob": "^7.1.1",
+        "lodash": "^4.17.10",
+        "require-package-name": "^2.0.1"
+      }
+    },
     "babel-plugin-strip-function-call": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/babel-plugin-strip-function-call/-/babel-plugin-strip-function-call-1.0.2.tgz",
@@ -5246,7 +5259,8 @@
         "ansi-regex": {
           "version": "2.1.1",
           "resolved": false,
-          "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8="
+          "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8=",
+          "optional": true
         },
         "aproba": {
           "version": "1.2.0",
@@ -5267,12 +5281,14 @@
         "balanced-match": {
           "version": "1.0.0",
           "resolved": false,
-          "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c="
+          "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=",
+          "optional": true
         },
         "brace-expansion": {
           "version": "1.1.11",
           "resolved": false,
           "integrity": "sha512-iCuPHDFgrHX7H2vEI/5xpz07zSHB00TpugqhmYtVmMO6518mCuRMoOYFldEBl0g187ufozdaHgWKcYFb61qGiA==",
+          "optional": true,
           "requires": {
             "balanced-match": "^1.0.0",
             "concat-map": "0.0.1"
@@ -5287,17 +5303,20 @@
         "code-point-at": {
           "version": "1.1.0",
           "resolved": false,
-          "integrity": "sha1-DQcLTQQ6W+ozovGkDi7bPZpMz3c="
+          "integrity": "sha1-DQcLTQQ6W+ozovGkDi7bPZpMz3c=",
+          "optional": true
         },
         "concat-map": {
           "version": "0.0.1",
           "resolved": false,
-          "integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s="
+          "integrity": "sha1-2Klr13/Wjfd5OnMDajug1UBdR3s=",
+          "optional": true
         },
         "console-control-strings": {
           "version": "1.1.0",
           "resolved": false,
-          "integrity": "sha1-PXz0Rk22RG6mRL9LOVB/mFEAjo4="
+          "integrity": "sha1-PXz0Rk22RG6mRL9LOVB/mFEAjo4=",
+          "optional": true
         },
         "core-util-is": {
           "version": "1.0.2",
@@ -5414,7 +5433,8 @@
         "inherits": {
           "version": "2.0.3",
           "resolved": false,
-          "integrity": "sha1-Yzwsg+PaQqUC9SRmAiSA9CCCYd4="
+          "integrity": "sha1-Yzwsg+PaQqUC9SRmAiSA9CCCYd4=",
+          "optional": true
         },
         "ini": {
           "version": "1.3.5",
@@ -5426,6 +5446,7 @@
           "version": "1.0.0",
           "resolved": false,
           "integrity": "sha1-754xOG8DGn8NZDr4L95QxFfvAMs=",
+          "optional": true,
           "requires": {
             "number-is-nan": "^1.0.0"
           }
@@ -5440,6 +5461,7 @@
           "version": "3.0.4",
           "resolved": false,
           "integrity": "sha512-yJHVQEhyqPLUTgt9B83PXu6W3rx4MvvHvSUvToogpwoGDOUQ+yDrR0HRot+yOCdCO7u4hX3pWft6kWBBcqh0UA==",
+          "optional": true,
           "requires": {
             "brace-expansion": "^1.1.7"
           }
@@ -5447,12 +5469,14 @@
         "minimist": {
           "version": "0.0.8",
           "resolved": false,
-          "integrity": "sha1-hX/Kv8M5fSYluCKCYuhqp6ARsF0="
+          "integrity": "sha1-hX/Kv8M5fSYluCKCYuhqp6ARsF0=",
+          "optional": true
         },
         "minipass": {
           "version": "2.3.5",
           "resolved": false,
           "integrity": "sha512-Gi1W4k059gyRbyVUZQ4mEqLm0YIUiGYfvxhF6SIlk3ui1WVxMTGfGdQ2SInh3PDrRTVvPKgULkpJtT4RH10+VA==",
+          "optional": true,
           "requires": {
             "safe-buffer": "^5.1.2",
             "yallist": "^3.0.0"
@@ -5471,6 +5495,7 @@
           "version": "0.5.1",
           "resolved": false,
           "integrity": "sha1-MAV0OOrGz3+MR2fzhkjWaX11yQM=",
+          "optional": true,
           "requires": {
             "minimist": "0.0.8"
           }
@@ -5551,7 +5576,8 @@
         "number-is-nan": {
           "version": "1.0.1",
           "resolved": false,
-          "integrity": "sha1-CXtgK1NCKlIsGvuHkDGDNpQaAR0="
+          "integrity": "sha1-CXtgK1NCKlIsGvuHkDGDNpQaAR0=",
+          "optional": true
         },
         "object-assign": {
           "version": "4.1.1",
@@ -5563,6 +5589,7 @@
           "version": "1.4.0",
           "resolved": false,
           "integrity": "sha1-WDsap3WWHUsROsF9nFC6753Xa9E=",
+          "optional": true,
           "requires": {
             "wrappy": "1"
           }
@@ -5648,7 +5675,8 @@
         "safe-buffer": {
           "version": "5.1.2",
           "resolved": false,
-          "integrity": "sha512-Gd2UZBJDkXlY7GbJxfsE8/nvKkUEU1G38c1siN6QP6a9PT9MmHB8GnpscSmMJSoF8LOIrt8ud/wPtojys4G6+g=="
+          "integrity": "sha512-Gd2UZBJDkXlY7GbJxfsE8/nvKkUEU1G38c1siN6QP6a9PT9MmHB8GnpscSmMJSoF8LOIrt8ud/wPtojys4G6+g==",
+          "optional": true
         },
         "safer-buffer": {
           "version": "2.1.2",
@@ -5684,6 +5712,7 @@
           "version": "1.0.2",
           "resolved": false,
           "integrity": "sha1-EYvfW4zcUaKn5w0hHgfisLmxB9M=",
+          "optional": true,
           "requires": {
             "code-point-at": "^1.0.0",
             "is-fullwidth-code-point": "^1.0.0",
@@ -5703,6 +5732,7 @@
           "version": "3.0.1",
           "resolved": false,
           "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
+          "optional": true,
           "requires": {
             "ansi-regex": "^2.0.0"
           }
@@ -5746,12 +5776,14 @@
         "wrappy": {
           "version": "1.0.2",
           "resolved": false,
-          "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
+          "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=",
+          "optional": true
         },
         "yallist": {
           "version": "3.0.3",
           "resolved": false,
-          "integrity": "sha512-S+Zk8DEWE6oKpV+vI3qWkaK+jSbIK86pCwe2IF/xwIpQ8jEuxpw9NyaGjmp9+BoJv5FV2piqCDcoCtStppiq2A=="
+          "integrity": "sha512-S+Zk8DEWE6oKpV+vI3qWkaK+jSbIK86pCwe2IF/xwIpQ8jEuxpw9NyaGjmp9+BoJv5FV2piqCDcoCtStppiq2A==",
+          "optional": true
         }
       }
     },
@@ -11190,6 +11222,12 @@
       "resolved": "https://registry.npmjs.org/require-main-filename/-/require-main-filename-2.0.0.tgz",
       "integrity": "sha512-NKN5kMDylKuldxYLSUfrbo5Tuzh4hd+2E8NPPX02mZtn1VuREQToYe/ZdlJy+J3uCpfaiGF05e7B8W0iXbQHmg=="
     },
+    "require-package-name": {
+      "version": "2.0.1",
+      "resolved": "https://registry.npmjs.org/require-package-name/-/require-package-name-2.0.1.tgz",
+      "integrity": "sha1-wR6XJ2tluOKSP3Xav1+y7ww4Qbk=",
+      "dev": true
+    },
     "resolve": {
       "version": "1.11.1",
       "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.11.1.tgz",
diff --git a/package.json b/package.json
index a7a4acb9c..33232a64a 100644
--- a/package.json
+++ b/package.json
@@ -121,6 +121,7 @@
     "yaml-front-matter": "^4.0.0"
   },
   "devDependencies": {
+    "babel-plugin-lodash": "^3.3.4",
     "chai": "^4.1.2",
     "chai-http": "^4.0.0",
     "eslint": "^5.14.1",

From b8263a2fe285104877a1df6f0cbc81d49cb27ef8 Mon Sep 17 00:00:00 2001
From: raftar2097 <ragarwala2097@gmail.com>
Date: Mon, 30 Mar 2020 20:37:37 +0530
Subject: [PATCH 11/30] Update index.js

Replaced "require" with "import"
---
 src/index.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/index.js b/src/index.js
index b8b666172..cbbcdf57b 100644
--- a/src/index.js
+++ b/src/index.js
@@ -9,6 +9,7 @@ import { Provider } from "react-redux";
 /* A U S P I C E   I M P O R T S */
 import configureStore from "./store";
 import { initialiseGoogleAnalyticsIfRequired } from "./util/googleAnalytics";
+import Root from "./root";
 /* S T Y L E S H E E T S */
 import "font-awesome/css/font-awesome.css";
 import "leaflet/dist/leaflet.css";
@@ -35,7 +36,6 @@ initialiseGoogleAnalyticsIfRequired();
 /* Using React Hot Loader 4 https://github.com/gaearon/react-hot-loader */
 
 const renderApp = () => {
-  const Root = require("./root").default; // eslint-disable-line global-require
   ReactDOM.render(
     <Provider store={store}>
       <Root />

From b1be7a727546bda618b3288b672917e16c197a56 Mon Sep 17 00:00:00 2001
From: Avin <avinkavesha@gmail.com>
Date: Thu, 2 Apr 2020 08:32:45 +0530
Subject: [PATCH 12/30] Move babel-plugin-lodash to dependencies

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 33232a64a..5bed4f93d 100644
--- a/package.json
+++ b/package.json
@@ -46,6 +46,7 @@
     "awesomplete": "^1.1.2",
     "babel-eslint": "^10.0.1",
     "babel-loader": "^8.0.4",
+    "babel-plugin-lodash": "^3.3.4",
     "babel-plugin-strip-function-call": "^1.0.2",
     "babel-plugin-styled-components": "^1.10.0",
     "babel-plugin-syntax-dynamic-import": "^6.18.0",
@@ -121,7 +122,6 @@
     "yaml-front-matter": "^4.0.0"
   },
   "devDependencies": {
-    "babel-plugin-lodash": "^3.3.4",
     "chai": "^4.1.2",
     "chai-http": "^4.0.0",
     "eslint": "^5.14.1",

From 5de5f98985c45808396af63e63180d393dc4733f Mon Sep 17 00:00:00 2001
From: joachimschmidt557 <joachim.schmidt557@outlook.com>
Date: Fri, 3 Apr 2020 18:30:56 +0200
Subject: [PATCH 13/30] fix map play and reset buttons

---
 src/components/map/map.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/components/map/map.js b/src/components/map/map.js
index 4b6fe8277..da3a39766 100644
--- a/src/components/map/map.js
+++ b/src/components/map/map.js
@@ -524,20 +524,20 @@ class Map extends React.Component {
       padding: 12,
       border: "none",
       zIndex: 900,
-      position: "absolute",
+      position: "relative",
       textTransform: "uppercase"
     };
     if (this.props.branchLengthsToDisplay !== "divOnly") {
       return (
-        <div>
+        <div style={{position: "absolute"}}>
           <button
-            style={{...buttonBaseStyle, top: 20, left: 20, width: 60, backgroundColor: this.props.animationPlayPauseButton === "Pause" ? pauseColor : goColor}}
+            style={{...buttonBaseStyle, top: 20, left: 20, backgroundColor: this.props.animationPlayPauseButton === "Pause" ? pauseColor : goColor}}
             onClick={this.playPauseButtonClicked}
           >
             {this.props.t(this.props.animationPlayPauseButton)}
           </button>
           <button
-            style={{...buttonBaseStyle, top: 20, left: 88, width: 60, backgroundColor: lightGrey}}
+            style={{...buttonBaseStyle, top: 20, left: 30, backgroundColor: lightGrey}}
             onClick={this.resetButtonClicked}
           >
             {this.props.t("Reset")}

From b553a323fd4601c43fa66b7b50b4a3bd72eb15cb Mon Sep 17 00:00:00 2001
From: Maxwell Zimon <max@zimon.co>
Date: Sun, 5 Apr 2020 10:52:58 -0500
Subject: [PATCH 14/30] #915: determine whether tip label should be shown based
 on count of fully visible nodes, not all in-view nodes

---
 src/components/tree/phyloTree/labels.js | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/components/tree/phyloTree/labels.js b/src/components/tree/phyloTree/labels.js
index 8e67935bc..4e6e90437 100644
--- a/src/components/tree/phyloTree/labels.js
+++ b/src/components/tree/phyloTree/labels.js
@@ -13,8 +13,11 @@ export const updateTipLabels = function updateTipLabels(dt) {
   const yPad = this.params.tipLabelPadY;
   const inViewTerminalNodes = this.nodes
     .filter((d) => d.terminal)
-    .filter((d) => d.inView);
+    .filter((d) => d.inView)
+    .filter((d) => d.visibility == NODE_VISIBLE);
+
   // console.log(`there are ${inViewTerminalNodes.length} nodes in view`)
+  
   if (inViewTerminalNodes.length < this.params.tipLabelBreakL1) {
 
     let fontSize = this.params.tipLabelFontSizeL1;

From 2acff616e400c13ec79be6e0ccccbc9906db6ffb Mon Sep 17 00:00:00 2001
From: Maxwell Zimon <max@zimon.co>
Date: Sun, 5 Apr 2020 11:41:23 -0500
Subject: [PATCH 15/30] #915: using triple equals

---
 src/components/tree/phyloTree/labels.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/tree/phyloTree/labels.js b/src/components/tree/phyloTree/labels.js
index 4e6e90437..d92918064 100644
--- a/src/components/tree/phyloTree/labels.js
+++ b/src/components/tree/phyloTree/labels.js
@@ -14,7 +14,7 @@ export const updateTipLabels = function updateTipLabels(dt) {
   const inViewTerminalNodes = this.nodes
     .filter((d) => d.terminal)
     .filter((d) => d.inView)
-    .filter((d) => d.visibility == NODE_VISIBLE);
+    .filter((d) => d.visibility === NODE_VISIBLE);
 
   // console.log(`there are ${inViewTerminalNodes.length} nodes in view`)
   

From b6c6449e661637121876d35a2b0639198c288f67 Mon Sep 17 00:00:00 2001
From: Haruka Iwao <yuryu@yuryu.jp>
Date: Sun, 5 Apr 2020 23:18:09 -0700
Subject: [PATCH 16/30] Add Japanese localization - WIP

---
 src/locales/ja/language.json    |  3 ++
 src/locales/ja/sidebar.json     | 32 +++++++++++
 src/locales/ja/translation.json | 96 +++++++++++++++++++++++++++++++++
 3 files changed, 131 insertions(+)
 create mode 100644 src/locales/ja/language.json
 create mode 100644 src/locales/ja/sidebar.json
 create mode 100644 src/locales/ja/translation.json

diff --git a/src/locales/ja/language.json b/src/locales/ja/language.json
new file mode 100644
index 000000000..4945a2d33
--- /dev/null
+++ b/src/locales/ja/language.json
@@ -0,0 +1,3 @@
+{
+    "name": "日本語"
+}
\ No newline at end of file
diff --git a/src/locales/ja/sidebar.json b/src/locales/ja/sidebar.json
new file mode 100644
index 000000000..be0c478bc
--- /dev/null
+++ b/src/locales/ja/sidebar.json
@@ -0,0 +1,32 @@
+{
+  "Dataset": "Dataset",
+  "Date Range": "Date Range",
+  "Color By": "Color By",
+  "Tree Options": "Tree Options",
+  "Layout": "Layout",
+  "rectangular": "rectangular",
+  "radial": "radial",
+  "unrooted": "unrooted",
+  "clock": "clock",
+  "Branch Length": "Branch Length",
+  "time": "time",
+  "divergence": "divergence",
+  "Branch Labels": "Branch Labels",
+  "Search Strains": "Search Strains",
+  "Second Tree": "Second Tree",
+  "Map Options": "Map Options",
+  "Geographic resolution": "Geographic resolution",
+  "Animation Speed": "Animation Speed",
+  "Loop animation": "Loop animation",
+  "Animate cumulative history": "Animate cumulative history",
+  "Panel Options": "Panel Options",
+  "Show tree": "Show tree",
+  "Show map": "Show map",
+  "Show entropy": "Show entropy",
+  "Language": "Language",
+  "Slow": "Slow",
+  "Medium": "Medium",
+  "Fast": "Fast",
+  "full": "full",
+  "grid": "grid"
+}
\ No newline at end of file
diff --git a/src/locales/ja/translation.json b/src/locales/ja/translation.json
new file mode 100644
index 000000000..2d8f452b0
--- /dev/null
+++ b/src/locales/ja/translation.json
@@ -0,0 +1,96 @@
+{
+  "__Header//Byline__": "########################################",
+  "Maintained by": "管理者",
+  "using data from": "使用データ",
+  "Built with": "Built with",
+
+
+  "__Header//Info__": "########################################",
+  "Showing {{x}} of {{y}} genomes": "表示中: {{x}} 中 {{y}} のゲノム",
+  "sampled between {{from}} and {{to}}": "サンプル期間 {{from}} から {{to}}",
+  "and comprising": "and comprising",
+  "comprising": "comprising",
+  "Animation in progress.": "アニメーション中.",
+  "Filtered to": "フィルター条件",
+  "__Header//Info__": "########################################",
+  "Showing {{x}} of {{y}} genomes.": "Showing {{x}} of {{y}} genomes.",
+  "Showing {{x}} of {{y}} genomes sampled between {{from}} and {{to}}.": "Showing {{x}} of {{y}} genomes sampled between {{from}} and {{to}}.",
+  "Comprising": "Comprising",
+  "Animation in progress.": "Animation in progress.",
+  "Filtered to": "Filtered to",
+
+  "__Download Modal__": "########################################",
+  "click outside this box to return to the app": "元の画面に戻るにはこのポップアップの外側をクリック",
+  "last updated": "最終更新",
+  "A full list of sequence authors is available via the TSV files below.": "シーケンス作成者の完全な一覧は、TSVファイルとしてもダウンロードできます。",
+  "Data usage policy": "データ利用ポリシー",
+  "Please cite the authors who contributed genomic data (where relevant), as well as:": "遺伝子データを貢献した作者を明記してすること。Please cite the authors who contributed genomic data (where relevant), as well as:",
+  "Download data": "データをダウンロード",
+  "Data usage part 1": "The data presented here is intended to rapidly disseminate analysis of important pathogens. Unpublished data is included with permission of the data generators, and does not impact their right to publish. ",
+  "Data usage part 2": "Please contact the respective authors (available via the TSV files below) if you intend to carry out further research using their data. Derived data, such as phylogenies, can be downloaded below - please contact the relevant authors where appropriate.",
+
+  "__Entropy Panel__": "########################################",
+  "Diversity": "",
+  "entropy": "エントロピー",
+  "events": "イベント",
+  "Codon {{codon}} in protein {{protein}}": "タンパク質 {{protein}} に含まれるコドン {{codon}}",
+  "Nucleotide {{nuc}}": "ヌクレオチド {{nuc}}",
+  "Nuc positions {{a}} to {{b}}": "ヌクレオチド位置 {{a}} から {{b}}",
+  "Num mutations": "変異数",
+  "Negative strand": "負のらせん",
+  "Positive strand": "正のらせん",
+  "Click to color tree & map": "クリックしてツリーと地図を色分けする",
+
+
+  "__Footer__": "########################################",
+  "Filter by {{filterTitle}}": "フィルタ条件 {{filterTitle}}",
+  "Data updated": "データ更新",
+
+
+  "__Map panel__": "########################################",
+  "Transmissions": "伝搬",
+  "Geography": "地理",
+  "reset zoom": "標準倍率",
+  "Reset": "リセット",
+  "Play": "再生",
+  "Pause": "一時停止",
+
+
+  "__Tree (Phylogeny) panel__": "########################################",
+  "Phylogeny": "発生系統",
+  "Reset Layout": "レイアウトをリセット",
+  "Click on tip to display more info": "詳細を表示するには吹き出しをクリック",
+  "Click to zoom into clade": "クリックして分岐群へズーム",
+  "Branch leading to": "枝分かれ先",
+  "Number of descendants": "子孫数",
+  "Nucleotide mutations": "ヌクレオチド変異",
+  "AA mutations": "AA mutations",
+  "protein mutations truncated": "protein mutations truncated",
+  "Gaps": "Gaps",
+  "more": "more",
+  "No nucleotide mutations": "No nucleotide mutations",
+  "No amino acid mutations": "No amino acid mutations",
+  "Divergence": "Divergence",
+  "Date": "日付",
+  "Collection date": "Collection date",
+  "Inferred collection date": "Inferred collection date",
+  "Inferred Date": "Inferred Date",
+  "Date Confidence Interval": "Date Confidence Interval",
+  "Vaccine selected": "Vaccine selected",
+  "Vaccine start date": "Vaccine start date",
+  "Vaccine end date": "Vaccine end date",
+  "Serum strain": "Serum strain",
+  "Click outside this box to go back to the tree": "Click outside this box to go back to the tree",
+  "Authors": "作成者",
+  "Title": "タイトル",
+  "Journal": "ジャーナル",
+
+
+  "__Frequencies panel__": "########################################",
+  "Frequencies": "頻度",
+  "colored by": "色分け条件",
+  "Projection": "射影",
+  "Time point": "Time point",
+  "Frequency": "Frequency",
+  "Projected frequency": "Projected frequency"
+}
\ No newline at end of file

From 5da0adb2769f66b0879bcf311330175f339d41f5 Mon Sep 17 00:00:00 2001
From: Emma Haruka Iwao <yuryu@google.com>
Date: Tue, 7 Apr 2020 13:29:37 -0700
Subject: [PATCH 17/30] Add Japanese translation

---
 src/components/controls/language.js |  3 +-
 src/locales/ja/translation.json     | 65 +++++++++++++----------------
 2 files changed, 32 insertions(+), 36 deletions(-)

diff --git a/src/components/controls/language.js b/src/components/controls/language.js
index b1b9c0fda..ebc3ac240 100644
--- a/src/components/controls/language.js
+++ b/src/components/controls/language.js
@@ -29,7 +29,8 @@ class Language extends React.Component {
       {value: "ru", label: "Русский"},
       {value: "lt", label: "Lietuvių"},
       {value: "pt", label: "Português"},
-      {value: "fr", label: "Français"}
+      {value: "fr", label: "Français"},
+      {value: "ja", label: "日本語"},
     ];
     return languages;
   }
diff --git a/src/locales/ja/translation.json b/src/locales/ja/translation.json
index 2d8f452b0..307e726db 100644
--- a/src/locales/ja/translation.json
+++ b/src/locales/ja/translation.json
@@ -6,31 +6,25 @@
 
 
   "__Header//Info__": "########################################",
-  "Showing {{x}} of {{y}} genomes": "表示中: {{x}} 中 {{y}} のゲノム",
-  "sampled between {{from}} and {{to}}": "サンプル期間 {{from}} から {{to}}",
-  "and comprising": "and comprising",
-  "comprising": "comprising",
-  "Animation in progress.": "アニメーション中.",
-  "Filtered to": "フィルター条件",
-  "__Header//Info__": "########################################",
-  "Showing {{x}} of {{y}} genomes.": "Showing {{x}} of {{y}} genomes.",
-  "Showing {{x}} of {{y}} genomes sampled between {{from}} and {{to}}.": "Showing {{x}} of {{y}} genomes sampled between {{from}} and {{to}}.",
-  "Comprising": "Comprising",
-  "Animation in progress.": "Animation in progress.",
-  "Filtered to": "Filtered to",
+  "Showing {{x}} of {{y}} genomes": "{{y}} 中 {{x}} のゲノムを表示中",
+  "Showing {{x}} of {{y}} genomes sampled between {{from}} and {{to}}": "{{y}} 中 {{x}} の {{from}} から {{to}} にサンプルされたゲノムを表示中",
+  "Comprising": "次を含む",
+  "Animation in progress": "アニメーション中",
+  "Filtered to": "フィルタ条件",
+
 
   "__Download Modal__": "########################################",
   "click outside this box to return to the app": "元の画面に戻るにはこのポップアップの外側をクリック",
   "last updated": "最終更新",
   "A full list of sequence authors is available via the TSV files below.": "シーケンス作成者の完全な一覧は、TSVファイルとしてもダウンロードできます。",
   "Data usage policy": "データ利用ポリシー",
-  "Please cite the authors who contributed genomic data (where relevant), as well as:": "遺伝子データを貢献した作者を明記してすること。Please cite the authors who contributed genomic data (where relevant), as well as:",
+  "Please cite the authors who contributed genomic data (where relevant), as well as": "次の貢献者と、(該当する場合)遺伝子データを貢献した作者を明記すること",
   "Download data": "データをダウンロード",
-  "Data usage part 1": "The data presented here is intended to rapidly disseminate analysis of important pathogens. Unpublished data is included with permission of the data generators, and does not impact their right to publish. ",
-  "Data usage part 2": "Please contact the respective authors (available via the TSV files below) if you intend to carry out further research using their data. Derived data, such as phylogenies, can be downloaded below - please contact the relevant authors where appropriate.",
+  "Data usage part 1": "このデータは、重要な病原体の分析結果を迅速に広めるために提供されている。出版されていないデータが生成者の許可のもと含まれているが、このことは生成者の出版権利に影響しない。",
+  "Data usage part 2": "もしダウンロードしたデータをもとにさらに研究を行う予定であれば、(TSVファイルに含まれる)該当する作者に連絡のこと。系統発生などの派生したデータは下記からダウンロード可能 - 必要であれば該当する作者に連絡のこと。",
 
   "__Entropy Panel__": "########################################",
-  "Diversity": "",
+  "Diversity": "多様性",
   "entropy": "エントロピー",
   "events": "イベント",
   "Codon {{codon}} in protein {{protein}}": "タンパク質 {{protein}} に含まれるコドン {{codon}}",
@@ -43,7 +37,7 @@
 
 
   "__Footer__": "########################################",
-  "Filter by {{filterTitle}}": "フィルタ条件 {{filterTitle}}",
+  "Filter by {{filterTitle}}": "{{filterTitle}} でフィルタ",
   "Data updated": "データ更新",
 
 
@@ -61,26 +55,27 @@
   "Reset Layout": "レイアウトをリセット",
   "Click on tip to display more info": "詳細を表示するには吹き出しをクリック",
   "Click to zoom into clade": "クリックして分岐群へズーム",
+  "Click to zoom out to parent clade": "Click to zoom out to parent clade",
   "Branch leading to": "枝分かれ先",
   "Number of descendants": "子孫数",
   "Nucleotide mutations": "ヌクレオチド変異",
-  "AA mutations": "AA mutations",
-  "protein mutations truncated": "protein mutations truncated",
+  "AA mutations": "AA 変異",
+  "protein mutations truncated": "タンパク質変異は省略された",
   "Gaps": "Gaps",
-  "more": "more",
-  "No nucleotide mutations": "No nucleotide mutations",
-  "No amino acid mutations": "No amino acid mutations",
-  "Divergence": "Divergence",
+  "more": "さらに",
+  "No nucleotide mutations": "ヌクレオチド変異なし",
+  "No amino acid mutations": "アミノ酸変異なし",
+  "Divergence": "分岐",
   "Date": "日付",
-  "Collection date": "Collection date",
-  "Inferred collection date": "Inferred collection date",
-  "Inferred Date": "Inferred Date",
-  "Date Confidence Interval": "Date Confidence Interval",
-  "Vaccine selected": "Vaccine selected",
-  "Vaccine start date": "Vaccine start date",
-  "Vaccine end date": "Vaccine end date",
-  "Serum strain": "Serum strain",
-  "Click outside this box to go back to the tree": "Click outside this box to go back to the tree",
+  "Collection date": "収集日",
+  "Inferred collection date": "推定収集日",
+  "Inferred Date": "推定日",
+  "Date Confidence Interval": "日付の信頼区間",
+  "Vaccine selected": "選択されたワクチン",
+  "Vaccine start date": "ワクチン開始日",
+  "Vaccine end date": "ワクチン終了日",
+  "Serum strain": "血清株",
+  "Click outside this box to go back to the tree": "ツリーに戻るにはこのボックスの外側をクリック",
   "Authors": "作成者",
   "Title": "タイトル",
   "Journal": "ジャーナル",
@@ -90,7 +85,7 @@
   "Frequencies": "頻度",
   "colored by": "色分け条件",
   "Projection": "射影",
-  "Time point": "Time point",
-  "Frequency": "Frequency",
-  "Projected frequency": "Projected frequency"
+  "Time point": "基準時間",
+  "Frequency": "頻度",
+  "Projected frequency": "射影された頻度"
 }
\ No newline at end of file

From 1dd9537c6d350dbb753787933d11de9dcf9bf081 Mon Sep 17 00:00:00 2001
From: Haruka Iwao <yuryu@yuryu.jp>
Date: Sun, 5 Apr 2020 23:18:09 -0700
Subject: [PATCH 18/30] Add Japanese translation

---
 src/components/controls/language.js |  3 +-
 src/locales/ja/language.json        |  3 +
 src/locales/ja/sidebar.json         | 32 ++++++++++
 src/locales/ja/translation.json     | 91 +++++++++++++++++++++++++++++
 4 files changed, 128 insertions(+), 1 deletion(-)
 create mode 100644 src/locales/ja/language.json
 create mode 100644 src/locales/ja/sidebar.json
 create mode 100644 src/locales/ja/translation.json

diff --git a/src/components/controls/language.js b/src/components/controls/language.js
index b1b9c0fda..ebc3ac240 100644
--- a/src/components/controls/language.js
+++ b/src/components/controls/language.js
@@ -29,7 +29,8 @@ class Language extends React.Component {
       {value: "ru", label: "Русский"},
       {value: "lt", label: "Lietuvių"},
       {value: "pt", label: "Português"},
-      {value: "fr", label: "Français"}
+      {value: "fr", label: "Français"},
+      {value: "ja", label: "日本語"},
     ];
     return languages;
   }
diff --git a/src/locales/ja/language.json b/src/locales/ja/language.json
new file mode 100644
index 000000000..4945a2d33
--- /dev/null
+++ b/src/locales/ja/language.json
@@ -0,0 +1,3 @@
+{
+    "name": "日本語"
+}
\ No newline at end of file
diff --git a/src/locales/ja/sidebar.json b/src/locales/ja/sidebar.json
new file mode 100644
index 000000000..be0c478bc
--- /dev/null
+++ b/src/locales/ja/sidebar.json
@@ -0,0 +1,32 @@
+{
+  "Dataset": "Dataset",
+  "Date Range": "Date Range",
+  "Color By": "Color By",
+  "Tree Options": "Tree Options",
+  "Layout": "Layout",
+  "rectangular": "rectangular",
+  "radial": "radial",
+  "unrooted": "unrooted",
+  "clock": "clock",
+  "Branch Length": "Branch Length",
+  "time": "time",
+  "divergence": "divergence",
+  "Branch Labels": "Branch Labels",
+  "Search Strains": "Search Strains",
+  "Second Tree": "Second Tree",
+  "Map Options": "Map Options",
+  "Geographic resolution": "Geographic resolution",
+  "Animation Speed": "Animation Speed",
+  "Loop animation": "Loop animation",
+  "Animate cumulative history": "Animate cumulative history",
+  "Panel Options": "Panel Options",
+  "Show tree": "Show tree",
+  "Show map": "Show map",
+  "Show entropy": "Show entropy",
+  "Language": "Language",
+  "Slow": "Slow",
+  "Medium": "Medium",
+  "Fast": "Fast",
+  "full": "full",
+  "grid": "grid"
+}
\ No newline at end of file
diff --git a/src/locales/ja/translation.json b/src/locales/ja/translation.json
new file mode 100644
index 000000000..307e726db
--- /dev/null
+++ b/src/locales/ja/translation.json
@@ -0,0 +1,91 @@
+{
+  "__Header//Byline__": "########################################",
+  "Maintained by": "管理者",
+  "using data from": "使用データ",
+  "Built with": "Built with",
+
+
+  "__Header//Info__": "########################################",
+  "Showing {{x}} of {{y}} genomes": "{{y}} 中 {{x}} のゲノムを表示中",
+  "Showing {{x}} of {{y}} genomes sampled between {{from}} and {{to}}": "{{y}} 中 {{x}} の {{from}} から {{to}} にサンプルされたゲノムを表示中",
+  "Comprising": "次を含む",
+  "Animation in progress": "アニメーション中",
+  "Filtered to": "フィルタ条件",
+
+
+  "__Download Modal__": "########################################",
+  "click outside this box to return to the app": "元の画面に戻るにはこのポップアップの外側をクリック",
+  "last updated": "最終更新",
+  "A full list of sequence authors is available via the TSV files below.": "シーケンス作成者の完全な一覧は、TSVファイルとしてもダウンロードできます。",
+  "Data usage policy": "データ利用ポリシー",
+  "Please cite the authors who contributed genomic data (where relevant), as well as": "次の貢献者と、(該当する場合)遺伝子データを貢献した作者を明記すること",
+  "Download data": "データをダウンロード",
+  "Data usage part 1": "このデータは、重要な病原体の分析結果を迅速に広めるために提供されている。出版されていないデータが生成者の許可のもと含まれているが、このことは生成者の出版権利に影響しない。",
+  "Data usage part 2": "もしダウンロードしたデータをもとにさらに研究を行う予定であれば、(TSVファイルに含まれる)該当する作者に連絡のこと。系統発生などの派生したデータは下記からダウンロード可能 - 必要であれば該当する作者に連絡のこと。",
+
+  "__Entropy Panel__": "########################################",
+  "Diversity": "多様性",
+  "entropy": "エントロピー",
+  "events": "イベント",
+  "Codon {{codon}} in protein {{protein}}": "タンパク質 {{protein}} に含まれるコドン {{codon}}",
+  "Nucleotide {{nuc}}": "ヌクレオチド {{nuc}}",
+  "Nuc positions {{a}} to {{b}}": "ヌクレオチド位置 {{a}} から {{b}}",
+  "Num mutations": "変異数",
+  "Negative strand": "負のらせん",
+  "Positive strand": "正のらせん",
+  "Click to color tree & map": "クリックしてツリーと地図を色分けする",
+
+
+  "__Footer__": "########################################",
+  "Filter by {{filterTitle}}": "{{filterTitle}} でフィルタ",
+  "Data updated": "データ更新",
+
+
+  "__Map panel__": "########################################",
+  "Transmissions": "伝搬",
+  "Geography": "地理",
+  "reset zoom": "標準倍率",
+  "Reset": "リセット",
+  "Play": "再生",
+  "Pause": "一時停止",
+
+
+  "__Tree (Phylogeny) panel__": "########################################",
+  "Phylogeny": "発生系統",
+  "Reset Layout": "レイアウトをリセット",
+  "Click on tip to display more info": "詳細を表示するには吹き出しをクリック",
+  "Click to zoom into clade": "クリックして分岐群へズーム",
+  "Click to zoom out to parent clade": "Click to zoom out to parent clade",
+  "Branch leading to": "枝分かれ先",
+  "Number of descendants": "子孫数",
+  "Nucleotide mutations": "ヌクレオチド変異",
+  "AA mutations": "AA 変異",
+  "protein mutations truncated": "タンパク質変異は省略された",
+  "Gaps": "Gaps",
+  "more": "さらに",
+  "No nucleotide mutations": "ヌクレオチド変異なし",
+  "No amino acid mutations": "アミノ酸変異なし",
+  "Divergence": "分岐",
+  "Date": "日付",
+  "Collection date": "収集日",
+  "Inferred collection date": "推定収集日",
+  "Inferred Date": "推定日",
+  "Date Confidence Interval": "日付の信頼区間",
+  "Vaccine selected": "選択されたワクチン",
+  "Vaccine start date": "ワクチン開始日",
+  "Vaccine end date": "ワクチン終了日",
+  "Serum strain": "血清株",
+  "Click outside this box to go back to the tree": "ツリーに戻るにはこのボックスの外側をクリック",
+  "Authors": "作成者",
+  "Title": "タイトル",
+  "Journal": "ジャーナル",
+
+
+  "__Frequencies panel__": "########################################",
+  "Frequencies": "頻度",
+  "colored by": "色分け条件",
+  "Projection": "射影",
+  "Time point": "基準時間",
+  "Frequency": "頻度",
+  "Projected frequency": "射影された頻度"
+}
\ No newline at end of file

From 44c22a19247917abed2e3bf7efa6cacec49ab314 Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 14:05:31 +1200
Subject: [PATCH 19/30] Improve tree label font sizes

The font size should be a function of the total number of tips on the screen ("in-view"), regardless of their visibility. Renames variables to make the distinction clearer. There are still plenty of edge-cases where these don't look great, but this is a big improvement over the current version of auspice.
---
 src/components/tree/phyloTree/labels.js | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/components/tree/phyloTree/labels.js b/src/components/tree/phyloTree/labels.js
index d92918064..29348c509 100644
--- a/src/components/tree/phyloTree/labels.js
+++ b/src/components/tree/phyloTree/labels.js
@@ -11,27 +11,28 @@ export const updateTipLabels = function updateTipLabels(dt) {
   const tLFunc = this.callbacks.tipLabel;
   const xPad = this.params.tipLabelPadX;
   const yPad = this.params.tipLabelPadY;
-  const inViewTerminalNodes = this.nodes
+
+  const inViewTips = this.nodes
     .filter((d) => d.terminal)
-    .filter((d) => d.inView)
-    .filter((d) => d.visibility === NODE_VISIBLE);
+    .filter((d) => d.inView);
+
+  const inViewVisibleTips = inViewTips.filter((d) => d.visibility === NODE_VISIBLE);
 
-  // console.log(`there are ${inViewTerminalNodes.length} nodes in view`)
-  
-  if (inViewTerminalNodes.length < this.params.tipLabelBreakL1) {
+  /* We show tip labels by checking the number of "inView & visible" tips */
+  if (inViewVisibleTips.length < this.params.tipLabelBreakL1) {
 
+    /* We calculate font size based on the total number of in view tips (both visible & non-visible) */
     let fontSize = this.params.tipLabelFontSizeL1;
-    if (inViewTerminalNodes.length < this.params.tipLabelBreakL2) {
-      fontSize = this.params.tipLabelFontSizeL2;
-    }
-    if (inViewTerminalNodes.length < this.params.tipLabelBreakL3) {
+    if (inViewTips.length < this.params.tipLabelBreakL3) {
       fontSize = this.params.tipLabelFontSizeL3;
+    } else if (inViewTips.length < this.params.tipLabelBreakL2) {
+      fontSize = this.params.tipLabelFontSizeL2;
     }
 
     window.setTimeout(() => {
       this.groups.tipLabels
         .selectAll('.tipLabel')
-        .data(inViewTerminalNodes)
+        .data(inViewVisibleTips)
         .enter()
         .append("text")
         .attr("x", (d) => d.xTip + xPad)

From b3fa508009e500238ae9e42f915ce5bc89f1875b Mon Sep 17 00:00:00 2001
From: Emma Haruka Iwao <yuryu@google.com>
Date: Tue, 7 Apr 2020 20:23:14 -0700
Subject: [PATCH 20/30] Add missing Japanese translations

---
 src/components/tree/infoPanels/hover.js |  6 ++-
 src/locales/de/translation.json         |  2 +-
 src/locales/en/translation.json         |  2 +-
 src/locales/es/translation.json         |  2 +-
 src/locales/fr/translation.json         |  2 +-
 src/locales/ja/sidebar.json             | 61 +++++++++++++------------
 src/locales/ja/translation.json         | 10 ++--
 src/locales/lt/translation.json         |  2 +-
 src/locales/pt/translation.json         |  2 +-
 src/locales/ru/translation.json         |  2 +-
 10 files changed, 47 insertions(+), 44 deletions(-)

diff --git a/src/components/tree/infoPanels/hover.js b/src/components/tree/infoPanels/hover.js
index 27ab33c53..5dbd61c47 100644
--- a/src/components/tree/infoPanels/hover.js
+++ b/src/components/tree/infoPanels/hover.js
@@ -160,7 +160,9 @@ const Mutations = ({node, t}) => {
     const nucLen = nucs.length; // number of mutations that exist without N/-
 
     let m = nucs.slice(0, Math.min(nDisplay, nucLen)).join(", ");
-    m += nucLen > nDisplay ? " + " + (nucLen - nDisplay) + " " + t("more") : "";
+    if (nucLen > nDisplay) {
+      m += " + " + t("{{x}} more", {x: nucLen - nDisplay});
+    }
 
     if (nucLen !== 0) {
       elements.push(<InfoLine name={t("Nucleotide mutations")+":"} value={m} key="nuc"/>);
@@ -201,7 +203,7 @@ const Mutations = ({node, t}) => {
       if (idx < nProtsToDisplay) {
         let x = prot + ":\u00A0\u00A0" + mutationsToDisplay[prot].slice(0, Math.min(nDisplay, mutationsToDisplay[prot].length)).join(", ");
         if (mutationsToDisplay[prot].length > nDisplay) {
-          x += " + " + (mutationsToDisplay[prot].length - nDisplay) + " " + t("more");
+          x += " + " + t("{{x}} more", {x: mutationsToDisplay[prot].length - nDisplay});
         }
         mutationsToRender.push(x);
       } else if (idx === nProtsToDisplay) {
diff --git a/src/locales/de/translation.json b/src/locales/de/translation.json
index 9fe9716f7..c57855dd2 100644
--- a/src/locales/de/translation.json
+++ b/src/locales/de/translation.json
@@ -61,7 +61,7 @@
   "AA mutations": "AA-Mutationen",
   "protein mutations truncated": "Protein-Mutationen entfernt",
   "Gaps": "Lücken",
-  "more": "mehr",
+  "{{x}} more": "{{x}} mehr",
   "No nucleotide mutations": "Keine Nukleotid-Mutationen",
   "No amino acid mutations": "Keine Aminosäure-Mutationen",
   "Divergence": "Divergenz",
diff --git a/src/locales/en/translation.json b/src/locales/en/translation.json
index dc91867de..fdd43e64c 100644
--- a/src/locales/en/translation.json
+++ b/src/locales/en/translation.json
@@ -62,7 +62,7 @@
   "AA mutations": "AA mutations",
   "protein mutations truncated": "protein mutations truncated",
   "Gaps": "Gaps",
-  "more": "more",
+  "{{x}} more": "{{x}} more",
   "No nucleotide mutations": "No nucleotide mutations",
   "No amino acid mutations": "No amino acid mutations",
   "Divergence": "Divergence",
diff --git a/src/locales/es/translation.json b/src/locales/es/translation.json
index 968c59195..96ecf6465 100644
--- a/src/locales/es/translation.json
+++ b/src/locales/es/translation.json
@@ -59,7 +59,7 @@
   "AA mutations": "Mutaciones de AA",
   "protein mutations truncated": "mutaciones proteicas truncadas",
   "Gaps": "Huecos",
-  "more": "mas",
+  "{{x}} more": "{{x}} mas",
   "No nucleotide mutations": "No mutaciones de nucleótidos",
   "No amino acid mutations": "No mutaciones de aminoácidos",
   "Divergence": "Divergencia",
diff --git a/src/locales/fr/translation.json b/src/locales/fr/translation.json
index 756927d7f..32dc4e156 100644
--- a/src/locales/fr/translation.json
+++ b/src/locales/fr/translation.json
@@ -62,7 +62,7 @@
   "AA mutations": "Mutations de AA",
   "protein mutations truncated": "mutations protéiques tronquées",
   "Gaps": "Lacunes",
-  "more": "plus",
+  "{{x}} more": "{{x}} plus",
   "No nucleotide mutations": "Aucune mutation nucléotidique",
   "No amino acid mutations": "Aucune mutation d'acides aminés",
   "Divergence": "Divergence",
diff --git a/src/locales/ja/sidebar.json b/src/locales/ja/sidebar.json
index be0c478bc..a6d830af1 100644
--- a/src/locales/ja/sidebar.json
+++ b/src/locales/ja/sidebar.json
@@ -1,32 +1,33 @@
 {
-  "Dataset": "Dataset",
-  "Date Range": "Date Range",
-  "Color By": "Color By",
-  "Tree Options": "Tree Options",
-  "Layout": "Layout",
-  "rectangular": "rectangular",
-  "radial": "radial",
-  "unrooted": "unrooted",
-  "clock": "clock",
-  "Branch Length": "Branch Length",
-  "time": "time",
-  "divergence": "divergence",
-  "Branch Labels": "Branch Labels",
-  "Search Strains": "Search Strains",
-  "Second Tree": "Second Tree",
-  "Map Options": "Map Options",
-  "Geographic resolution": "Geographic resolution",
-  "Animation Speed": "Animation Speed",
-  "Loop animation": "Loop animation",
-  "Animate cumulative history": "Animate cumulative history",
-  "Panel Options": "Panel Options",
-  "Show tree": "Show tree",
-  "Show map": "Show map",
-  "Show entropy": "Show entropy",
-  "Language": "Language",
-  "Slow": "Slow",
-  "Medium": "Medium",
-  "Fast": "Fast",
-  "full": "full",
-  "grid": "grid"
+  "Dataset": "データセット",
+  "Date Range": "データ範囲",
+  "Color By": "色分け",
+  "Tree Options": "ツリーのオプション",
+  "Layout": "レイアウト",
+  "rectangular": "矩形",
+  "radial": "放射状",
+  "unrooted": "無根",
+  "clock": "時系列",
+  "Branch Length": "枝の長さ",
+  "time": "時間",
+  "divergence": "分岐",
+  "Show confidence intervals": "信頼区間を表示",
+  "Branch Labels": "枝のラベル",
+  "Search Strains": "系統を検索",
+  "Second Tree": "第二ツリー",
+  "Map Options": "地図のオプション",
+  "Geographic resolution": "地域分けの単位",
+  "Animation Speed": "アニメーション速度",
+  "Loop animation": "アニメーションを繰り返し",
+  "Animate cumulative history": "累積の履歴をアニメーション",
+  "Panel Options": "パネルのオプション",
+  "Show tree": "ツリーを表示",
+  "Show map": "地図を表示",
+  "Show entropy": "エントロピーを表示",
+  "Language": "言語",
+  "Slow": "遅い",
+  "Medium": "普通",
+  "Fast": "速い",
+  "full": "完全",
+  "grid": "グリッド"
 }
\ No newline at end of file
diff --git a/src/locales/ja/translation.json b/src/locales/ja/translation.json
index 307e726db..61bb30557 100644
--- a/src/locales/ja/translation.json
+++ b/src/locales/ja/translation.json
@@ -2,7 +2,7 @@
   "__Header//Byline__": "########################################",
   "Maintained by": "管理者",
   "using data from": "使用データ",
-  "Built with": "Built with",
+  "Built with": "使用ビルド",
 
 
   "__Header//Info__": "########################################",
@@ -16,7 +16,7 @@
   "__Download Modal__": "########################################",
   "click outside this box to return to the app": "元の画面に戻るにはこのポップアップの外側をクリック",
   "last updated": "最終更新",
-  "A full list of sequence authors is available via the TSV files below.": "シーケンス作成者の完全な一覧は、TSVファイルとしてもダウンロードできます。",
+  "A full list of sequence authors is available via the TSV files below": "シーケンス作成者の完全な一覧は、TSVファイルとしてもダウンロードできます",
   "Data usage policy": "データ利用ポリシー",
   "Please cite the authors who contributed genomic data (where relevant), as well as": "次の貢献者と、(該当する場合)遺伝子データを貢献した作者を明記すること",
   "Download data": "データをダウンロード",
@@ -55,14 +55,14 @@
   "Reset Layout": "レイアウトをリセット",
   "Click on tip to display more info": "詳細を表示するには吹き出しをクリック",
   "Click to zoom into clade": "クリックして分岐群へズーム",
-  "Click to zoom out to parent clade": "Click to zoom out to parent clade",
+  "Click to zoom out to parent clade": "親の分岐群にズームアウトするにはクリック",
   "Branch leading to": "枝分かれ先",
   "Number of descendants": "子孫数",
   "Nucleotide mutations": "ヌクレオチド変異",
   "AA mutations": "AA 変異",
   "protein mutations truncated": "タンパク質変異は省略された",
-  "Gaps": "Gaps",
-  "more": "さらに",
+  "Gaps": "間隔",
+  "{{x}} more": "他 {{x}}",
   "No nucleotide mutations": "ヌクレオチド変異なし",
   "No amino acid mutations": "アミノ酸変異なし",
   "Divergence": "分岐",
diff --git a/src/locales/lt/translation.json b/src/locales/lt/translation.json
index 8e9d5a95e..17889639f 100644
--- a/src/locales/lt/translation.json
+++ b/src/locales/lt/translation.json
@@ -62,7 +62,7 @@
   "AA mutations": "Amino rūgščių mutacijos",
   "protein mutations truncated": "baltymo mutacijos sutrumpintos",
   "Gaps": "Tarpai",
-  "more": "daugiau",
+  "{{x}} more": "{{x}} daugiau",
   "No nucleotide mutations": "Nėra nukelotidų mutacijų",
   "No amino acid mutations": "Nėra amino rūgščių mutacijų",
   "Divergence": "Skirtumas",
diff --git a/src/locales/pt/translation.json b/src/locales/pt/translation.json
index 290d5fb6e..a28a11c18 100644
--- a/src/locales/pt/translation.json
+++ b/src/locales/pt/translation.json
@@ -62,7 +62,7 @@
   "AA mutations": "Mutações de AA",
   "protein mutations truncated": "mutações proteicas truncadas",
   "Gaps": "Lacunas",
-  "more": "mais",
+  "{{x}} more": "{{x}} mais",
   "No nucleotide mutations": "Sem mutações nucleotídicas",
   "No amino acid mutations": "Sem mutações de aminoácidos",
   "Divergence": "Divergência",
diff --git a/src/locales/ru/translation.json b/src/locales/ru/translation.json
index 1b80809c1..b1fb03f8b 100644
--- a/src/locales/ru/translation.json
+++ b/src/locales/ru/translation.json
@@ -61,7 +61,7 @@
   "AA mutations": "Мутации Аминокислот",
   "protein mutations truncated": "мутации белков отображены неполностью",
   "Gaps": "Пробелы",
-  "more": "больше",
+  "{{x}} more": "{{x}} больше",
   "No nucleotide mutations": "Нет мутаций нуклеотидов",
   "No amino acid mutations": "Нет мутаций аминокислот",
   "Divergence": "Дивергенция",

From 5daee120d4f9194baa044ff9fc107060e292fbeb Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 15:53:32 +1200
Subject: [PATCH 21/30] Reinstate `lang` URL query

Initially i'd hoped to leave this out until we had unified language support across nextstrain.org, however it seems prudent to put this in now given the number of available translations in auspice
---
 src/middleware/changeURL.js | 10 ++++------
 src/reducers/general.js     | 11 +++--------
 2 files changed, 7 insertions(+), 14 deletions(-)

diff --git a/src/middleware/changeURL.js b/src/middleware/changeURL.js
index 6b3f52263..d2c8a1ce8 100644
--- a/src/middleware/changeURL.js
+++ b/src/middleware/changeURL.js
@@ -64,12 +64,10 @@ export const changeURLMiddleware = (store) => (next) => (action) => {
       query.r = action.data === state.controls.defaults.geoResolution ? undefined : action.data;
       break;
     }
-    /* The following has been commented out to give us time to check whether a `lang` query is
-    the appropriate way to set the language. This can be tracked via https://github.com/nextstrain/nextstrain.org/issues/130 */
-    // case types.CHANGE_LANGUAGE: {
-    //   query.lang = action.data === state.general.defaults.language ? undefined : action.data;
-    //   break;
-    // }
+    case types.CHANGE_LANGUAGE: {
+      query.lang = action.data === state.general.defaults.language ? undefined : action.data;
+      break;
+    }
     case types.CHANGE_DISTANCE_MEASURE: {
       query.m = action.data === state.controls.defaults.distanceMeasure ? undefined : action.data;
       break;
diff --git a/src/reducers/general.js b/src/reducers/general.js
index 667f03b63..e8428e2e7 100644
--- a/src/reducers/general.js
+++ b/src/reducers/general.js
@@ -1,4 +1,4 @@
-// import queryString from "query-string";
+import queryString from "query-string";
 import * as types from "../actions/types";
 import { chooseDisplayComponentFromURL } from "../actions/navigation";
 import { hasExtension, getExtension } from "../util/extensions";
@@ -7,9 +7,7 @@ import { hasExtension, getExtension } from "../util/extensions";
 not limited to <App>
 */
 
-/* See comment below for why this line is commented out -- it should be added back
-when a solution to https://github.com/nextstrain/nextstrain.org/issues/130 has been found */
-// const query = queryString.parse(window.location.search);
+const query = queryString.parse(window.location.search);
 
 const defaults = {
   language: "en"
@@ -28,10 +26,7 @@ const general = (state = {
   displayComponent: getFirstPageToDisplay(),
   errorMessage: undefined,
   pathname: window.location.pathname, // keep a copy of what the app "thinks" the pathname is
-  language: defaults.language
-  /* The following has been commented out to give us time to check whether a `lang` query is
-  the appropriate way to set the language. This can be tracked via https://github.com/nextstrain/nextstrain.org/issues/130 */
-  // language: query.lang ? query.lang : defaults.language
+  language: query.lang ? query.lang : defaults.language
 }, action) => {
   switch (action.type) {
     case types.PAGE_CHANGE:

From 971ee320a409506916cc360eee94b124779b594d Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 18:02:16 +1200
Subject: [PATCH 22/30] Keep legend open state in sync

This removes the "for" parameter, resulting in the open/close state of the legends being in-sync. I consider this a feature not a bug. Additionally, the code is simpler & the URL query for "legend" works again.
---
 src/components/map/map.js            | 2 +-
 src/components/tree/legend/legend.js | 6 +++---
 src/components/tree/tree.js          | 2 +-
 src/reducers/controls.js             | 5 +----
 4 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/src/components/map/map.js b/src/components/map/map.js
index 3334ad61d..c85b80c93 100644
--- a/src/components/map/map.js
+++ b/src/components/map/map.js
@@ -643,7 +643,7 @@ class Map extends React.Component {
     return (
       <Card center title={transmissionsExist ? "Transmissions" : "Geography"}>
         {this.props.legend && <ErrorBoundary>
-          <Legend right width={this.props.width} for="map" />
+          <Legend right width={this.props.width} />
         </ErrorBoundary>}
         {this.maybeCreateMapDiv()}
         {this.props.narrativeMode ? null : (
diff --git a/src/components/tree/legend/legend.js b/src/components/tree/legend/legend.js
index 0075a3c8a..0a06288a1 100644
--- a/src/components/tree/legend/legend.js
+++ b/src/components/tree/legend/legend.js
@@ -16,12 +16,12 @@ const svg = {
   userSelect: "none"
 };
 
-@connect((state, props) => {
+@connect((state) => {
   return {
     colorBy: state.controls.colorBy,
     colorings: state.metadata.colorings,
     colorScale: state.controls.colorScale,
-    legendOpen: props.for === "tree" ? state.controls.treeLegendOpen : state.controls.mapLegendOpen
+    legendOpen: state.controls.legendOpen
   };
 })
 class Legend extends React.Component {
@@ -85,7 +85,7 @@ class Legend extends React.Component {
   }
 
   toggleLegend() {
-    this.props.dispatch({type: TOGGLE_LEGEND, value: !this.props.legendOpen, for: this.props.for || "tree"});
+    this.props.dispatch({type: TOGGLE_LEGEND, value: !this.props.legendOpen});
   }
 
   /*
diff --git a/src/components/tree/tree.js b/src/components/tree/tree.js
index bf94a1c6e..b96eeb85c 100644
--- a/src/components/tree/tree.js
+++ b/src/components/tree/tree.js
@@ -126,7 +126,7 @@ class Tree extends React.Component {
     return (
       <Card center title={"Phylogeny"}>
         <ErrorBoundary>
-          <Legend width={this.props.width} for="tree"/>
+          <Legend width={this.props.width}/>
         </ErrorBoundary>
         <HoverInfoPanel
           hovered={this.state.hovered}
diff --git a/src/reducers/controls.js b/src/reducers/controls.js
index dadcbd019..421e44e0e 100644
--- a/src/reducers/controls.js
+++ b/src/reducers/controls.js
@@ -253,10 +253,7 @@ const Controls = (state = getDefaultControlsState(), action) => {
     case types.TOGGLE_SIDEBAR:
       return Object.assign({}, state, {sidebarOpen: action.value});
     case types.TOGGLE_LEGEND:
-      if (action.for === 'tree') {
-        return Object.assign({}, state, {treeLegendOpen: action.value});
-      }
-      return Object.assign({}, state, {mapLegendOpen: action.value});
+      return Object.assign({}, state, {legendOpen: action.value});
     case types.ADD_COLOR_BYS:
       for (const colorBy of Object.keys(action.newColorings)) {
         state.coloringsPresentOnTree.add(colorBy);

From 8acd76bfb95eb3acedf2f26c6cb10db622496b3d Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 19:21:33 +1200
Subject: [PATCH 23/30] add `lang` URL query to docs

---
 docs-src/docs/advanced-functionality/view-settings.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs-src/docs/advanced-functionality/view-settings.md b/docs-src/docs/advanced-functionality/view-settings.md
index 86db165eb..c72481461 100644
--- a/docs-src/docs/advanced-functionality/view-settings.md
+++ b/docs-src/docs/advanced-functionality/view-settings.md
@@ -58,6 +58,7 @@ All URL queries modify the view away from the default settings -- if you change
 | `r`        | Geographic resolution | `r=region` |
 | `m`        | Phylogeny x-axis measure | `m=div` |
 | `l`        | Phylogeny layout | `l=clock` |
+| `lang`     | Language | `lang=js` (Japanese) |
 | `dmin`     | Temporal range (minimum) | `dmin=2008-05-13` |
 | `dmax`     | Temporal range (maximum) | `dmax=2010-05-13` |
 | `f_<name>` | Data filter. Multiple values per key are `,` separated. | `f_region=Oceania` |

From 0bfc3f15dd9de03e66bc91205b8d0a6fec8009ad Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 19:22:57 +1200
Subject: [PATCH 24/30] typo

---
 docs-src/docs/advanced-functionality/view-settings.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs-src/docs/advanced-functionality/view-settings.md b/docs-src/docs/advanced-functionality/view-settings.md
index c72481461..42c0f9d10 100644
--- a/docs-src/docs/advanced-functionality/view-settings.md
+++ b/docs-src/docs/advanced-functionality/view-settings.md
@@ -58,7 +58,7 @@ All URL queries modify the view away from the default settings -- if you change
 | `r`        | Geographic resolution | `r=region` |
 | `m`        | Phylogeny x-axis measure | `m=div` |
 | `l`        | Phylogeny layout | `l=clock` |
-| `lang`     | Language | `lang=js` (Japanese) |
+| `lang`     | Language | `lang=ja` (Japanese) |
 | `dmin`     | Temporal range (minimum) | `dmin=2008-05-13` |
 | `dmax`     | Temporal range (maximum) | `dmax=2010-05-13` |
 | `f_<name>` | Data filter. Multiple values per key are `,` separated. | `f_region=Oceania` |

From 84fbe0f670220915e067f393ed1b2648ca0294f8 Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 19:43:01 +1200
Subject: [PATCH 25/30] Update package-lock via `npm audit fix`

---
 package-lock.json | 2784 +++++++++++++++++++++++++++++----------------
 1 file changed, 1792 insertions(+), 992 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 36fdd9baf..adb3de070 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "auspice",
-  "version": "2.11.1",
+  "version": "2.11.4",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
@@ -897,7 +897,6 @@
       "version": "1.0.4",
       "resolved": "https://registry.npmjs.org/@cnakazawa/watch/-/watch-1.0.4.tgz",
       "integrity": "sha512-v9kIhKwjeZThiWrLmj0y17CWoyddASLj9O2yvbZkbvw/N3rWOYy9zkV66ursAoVr0mV15bL8g0c4QZUE6cdDoQ==",
-      "dev": true,
       "requires": {
         "exec-sh": "^0.3.2",
         "minimist": "^1.2.0"
@@ -1021,14 +1020,14 @@
       "dev": true
     },
     "@jest/console": {
-      "version": "25.1.0",
-      "resolved": "https://registry.npmjs.org/@jest/console/-/console-25.1.0.tgz",
-      "integrity": "sha512-3P1DpqAMK/L07ag/Y9/Jup5iDEG9P4pRAuZiMQnU0JB3UOvCyYCjCoxr7sIA80SeyUCUKrr24fKAxVpmBgQonA==",
+      "version": "25.2.6",
+      "resolved": "https://registry.npmjs.org/@jest/console/-/console-25.2.6.tgz",
+      "integrity": "sha512-bGp+0PicZVCEhb+ifnW9wpKWONNdkhtJsRE7ap729hiAfTvCN6VhGx0s/l/V/skA2pnyqq+N/7xl9ZWfykDpsg==",
       "dev": true,
       "requires": {
-        "@jest/source-map": "^25.1.0",
+        "@jest/source-map": "^25.2.6",
         "chalk": "^3.0.0",
-        "jest-util": "^25.1.0",
+        "jest-util": "^25.2.6",
         "slash": "^3.0.0"
       },
       "dependencies": {
@@ -1084,212 +1083,41 @@
         }
       }
     },
-    "@jest/core": {
-      "version": "25.1.0",
-      "resolved": "https://registry.npmjs.org/@jest/core/-/core-25.1.0.tgz",
-      "integrity": "sha512-iz05+NmwCmZRzMXvMo6KFipW7nzhbpEawrKrkkdJzgytavPse0biEnCNr2wRlyCsp3SmKaEY+SGv7YWYQnIdig==",
-      "dev": true,
-      "requires": {
-        "@jest/console": "^25.1.0",
-        "@jest/reporters": "^25.1.0",
-        "@jest/test-result": "^25.1.0",
-        "@jest/transform": "^25.1.0",
-        "@jest/types": "^25.1.0",
-        "ansi-escapes": "^4.2.1",
-        "chalk": "^3.0.0",
-        "exit": "^0.1.2",
-        "graceful-fs": "^4.2.3",
-        "jest-changed-files": "^25.1.0",
-        "jest-config": "^25.1.0",
-        "jest-haste-map": "^25.1.0",
-        "jest-message-util": "^25.1.0",
-        "jest-regex-util": "^25.1.0",
-        "jest-resolve": "^25.1.0",
-        "jest-resolve-dependencies": "^25.1.0",
-        "jest-runner": "^25.1.0",
-        "jest-runtime": "^25.1.0",
-        "jest-snapshot": "^25.1.0",
-        "jest-util": "^25.1.0",
-        "jest-validate": "^25.1.0",
-        "jest-watcher": "^25.1.0",
-        "micromatch": "^4.0.2",
-        "p-each-series": "^2.1.0",
-        "realpath-native": "^1.1.0",
-        "rimraf": "^3.0.0",
-        "slash": "^3.0.0",
-        "strip-ansi": "^6.0.0"
-      },
-      "dependencies": {
-        "ansi-escapes": {
-          "version": "4.3.1",
-          "resolved": "https://registry.npmjs.org/ansi-escapes/-/ansi-escapes-4.3.1.tgz",
-          "integrity": "sha512-JWF7ocqNrp8u9oqpgV+wH5ftbt+cfvv+PTjOvKLT3AdYly/LmORARfEVT1iyjwN+4MqE5UmVKoAdIBqeoCHgLA==",
-          "dev": true,
-          "requires": {
-            "type-fest": "^0.11.0"
-          }
-        },
-        "ansi-regex": {
-          "version": "5.0.0",
-          "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.0.tgz",
-          "integrity": "sha512-bY6fj56OUQ0hU1KjFNDQuJFezqKdrAyFdIevADiqrWHwSlbmBNMHp5ak2f40Pm8JTFyM2mqxkG6ngkHO11f/lg==",
-          "dev": true
-        },
-        "ansi-styles": {
-          "version": "4.2.1",
-          "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.2.1.tgz",
-          "integrity": "sha512-9VGjrMsG1vePxcSweQsN20KY/c4zN0h9fLjqAbwbPfahM3t+NL+M9HC8xeXG2I8pX5NoamTGNuomEUFI7fcUjA==",
-          "dev": true,
-          "requires": {
-            "@types/color-name": "^1.1.1",
-            "color-convert": "^2.0.1"
-          }
-        },
-        "braces": {
-          "version": "3.0.2",
-          "resolved": "https://registry.npmjs.org/braces/-/braces-3.0.2.tgz",
-          "integrity": "sha512-b8um+L1RzM3WDSzvhm6gIz1yfTbBt6YTlcEKAvsmqCZZFw46z626lVj9j1yEPW33H5H+lBQpZMP1k8l+78Ha0A==",
-          "dev": true,
-          "requires": {
-            "fill-range": "^7.0.1"
-          }
-        },
-        "chalk": {
-          "version": "3.0.0",
-          "resolved": "https://registry.npmjs.org/chalk/-/chalk-3.0.0.tgz",
-          "integrity": "sha512-4D3B6Wf41KOYRFdszmDqMCGq5VV/uMAB273JILmO+3jAlh8X4qDtdtgCR3fxtbLEMzSx22QdhnDcJvu2u1fVwg==",
-          "dev": true,
-          "requires": {
-            "ansi-styles": "^4.1.0",
-            "supports-color": "^7.1.0"
-          }
-        },
-        "color-convert": {
-          "version": "2.0.1",
-          "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
-          "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
-          "dev": true,
-          "requires": {
-            "color-name": "~1.1.4"
-          }
-        },
-        "color-name": {
-          "version": "1.1.4",
-          "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
-          "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
-          "dev": true
-        },
-        "fill-range": {
-          "version": "7.0.1",
-          "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.0.1.tgz",
-          "integrity": "sha512-qOo9F+dMUmC2Lcb4BbVvnKJxTPjCm+RRpe4gDuGrzkL7mEVl/djYSu2OdQ2Pa302N4oqkSg9ir6jaLWJ2USVpQ==",
-          "dev": true,
-          "requires": {
-            "to-regex-range": "^5.0.1"
-          }
-        },
-        "graceful-fs": {
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@@ -13375,21 +14225,20 @@
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+      "resolved": "https://registry.npmjs.org/yargs/-/yargs-13.3.2.tgz",
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       "requires": {
-        "cliui": "^4.0.0",
+        "cliui": "^5.0.0",
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-        "os-locale": "^3.1.0",
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         "y18n": "^4.0.0",
-        "yargs-parser": "^13.0.0"
+        "yargs-parser": "^13.1.2"
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         "ansi-regex": {
@@ -13418,71 +14267,22 @@
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+      "version": "13.1.2",
+      "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.2.tgz",
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-            "y18n": "^3.2.1 || ^4.0.0",
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-      "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.4.1.tgz",
-      "integrity": "sha1-lSj0QtqxsihOWLQ3m7GU4i4MQAU=",
+      "version": "2.10.0",
+      "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.10.0.tgz",
+      "integrity": "sha1-x+sXyT4RLLEIb6bY5R+wZnt5pfk=",
       "dev": true,
       "requires": {
-        "fd-slicer": "~1.0.1"
+        "buffer-crc32": "~0.2.3",
+        "fd-slicer": "~1.1.0"
       }
     }
   }

From 044b7053af629ed0594d2d70cfa13fdee612889b Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 19:48:34 +1200
Subject: [PATCH 26/30] update dev docs

---
 DEV_DOCS.md | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/DEV_DOCS.md b/DEV_DOCS.md
index ff947985b..dec9d35fb 100644
--- a/DEV_DOCS.md
+++ b/DEV_DOCS.md
@@ -11,9 +11,15 @@ This project strictly adheres to the [Contributor Covenant Code of Conduct](http
 Please see the [project boards](https://github.com/orgs/nextstrain/projects) for currently available issues.
 
 ## Contributing code  
-[Please see the main auspice docs](https://nextstrain.github.io/auspice/introduction/install) for details on how to install and run auspice locally.
+Code contributions are welcomed! [Please see the main auspice docs](https://nextstrain.github.io/auspice/introduction/install) for details on how to install and run auspice from source. 
 
-For pull requests, please use [eslint](https://eslint.org/) as much as possible (via `npm run lint`).
+Please comment on an open issue if you are working on it.
+For changes unrelated to an open issue, please make an issue outlining what you would like to change/add.
+
+Please ensure there are no **linting** errors by running `npm run lint` (which uses [eslint](https://eslint.org/)).
+In the future we will make this a requirement for PRs or commits. 
+
+Where possible, **please rebase** your work onto master rather than merging changes from master into your PR.
 
 
 ## Contributing to Documentation

From e476fe37c2794a17f9adb0a1bd2780a766db2e7a Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 19:53:09 +1200
Subject: [PATCH 27/30] changelog

---
 CHANGELOG.md | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f69c14e48..e95db74fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,12 +2,19 @@
 title: Changelog
 ---
 
-## version 2.11.4 - 2020/04/04
+* Add a legend to the map! [See PR 935](https://github.com/nextstrain/auspice/pull/935)
+* Improve the animation smoothness, especially for datasets with limited temporal range. [See PR 920](https://github.com/nextstrain/auspice/pull/920)
+* Add Japanese translation [See PR 1045](https://github.com/nextstrain/auspice/pull/1045)
+* Reinstate the `lang` URL query to allow the URL to choose the language.
+* Remove unnecessary lodash code from the bundles. [See PR 1018](https://github.com/nextstrain/auspice/pull/1018)
+* Update how the `Root` component is imported. [See PR 1029](https://github.com/nextstrain/auspice/pull/1029)
+* Fix errors in the sizing of the map buttons. [See PR 1040](https://github.com/nextstrain/auspice/pull/1040)
+* Improve rendering of tree tip labels by only counting the selected (visible) tips. [See PR 1043](https://github.com/nextstrain/auspice/pull/1043)
 
+## version 2.11.4 - 2020/04/04
+* Temporarily remove SVG gradients in the tree due to bugs in multiple browsers. [See PR 1042](https://github.com/nextstrain/auspice/pull/1042)
 
 ## version 2.11.3 - 2020/04/02
-
-
 * Add Portuguese translation. [See PR 1017](https://github.com/nextstrain/auspice/pull/1017)
 * Fig bug where some branches would not display on certain browsers. [See PR 1022](https://github.com/nextstrain/auspice/pull/1022)
 * Fix bug with selected dates shown when no genomes were selected. [See PR 1011](https://github.com/nextstrain/auspice/pull/1011)

From 2284292030d349ec0aa1e8ed7c2c6eb504f93cb0 Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 20:00:19 +1200
Subject: [PATCH 28/30] version bump to 2.12.0 for release

---
 CHANGELOG.md   | 3 +++
 package.json   | 2 +-
 src/version.js | 2 +-
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e95db74fa..08d8ce8d8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,9 @@
 title: Changelog
 ---
 
+## version 2.12.0 - 2020/04/08
+
+
 * Add a legend to the map! [See PR 935](https://github.com/nextstrain/auspice/pull/935)
 * Improve the animation smoothness, especially for datasets with limited temporal range. [See PR 920](https://github.com/nextstrain/auspice/pull/920)
 * Add Japanese translation [See PR 1045](https://github.com/nextstrain/auspice/pull/1045)
diff --git a/package.json b/package.json
index ce074940a..9bdde19b0 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "auspice",
-  "version": "2.11.4",
+  "version": "2.12.0",
   "description": "Web app for visualizing pathogen evolution",
   "author": "James Hadfield, Trevor Bedford and Richard Neher",
   "license": "AGPL-3.0-only",
diff --git a/src/version.js b/src/version.js
index 40270b09f..10ec9ed13 100644
--- a/src/version.js
+++ b/src/version.js
@@ -1,4 +1,4 @@
-const version = "2.11.4";
+const version = "2.12.0";
 
 module.exports = {
   version

From 4402d587a4102950ba70bb2dead6a84a5a200db7 Mon Sep 17 00:00:00 2001
From: james hadfield <jh22@sanger.ac.uk>
Date: Wed, 8 Apr 2020 20:21:09 +1200
Subject: [PATCH 29/30] rebuild docs

---
 .../advanced-functionality/view-settings.html |  3 +-
 .../view-settings/index.html                  |  3 +-
 docs/contributing/overview.html               |  8 +++--
 docs/contributing/overview/index.html         |  8 +++--
 docs/releases/changelog.html                  | 36 +++++++++++++++++--
 docs/releases/changelog/index.html            | 36 +++++++++++++++++--
 docs/server/introduction.html                 |  4 +--
 docs/server/introduction/index.html           |  4 +--
 8 files changed, 86 insertions(+), 16 deletions(-)

diff --git a/docs/advanced-functionality/view-settings.html b/docs/advanced-functionality/view-settings.html
index 1e0ec5d65..e217390cc 100644
--- a/docs/advanced-functionality/view-settings.html
+++ b/docs/advanced-functionality/view-settings.html
@@ -109,6 +109,7 @@ <h2><a class="anchor" aria-hidden="true" id="url-query-options"></a><a href="#ur
 <tr><td><code>r</code></td><td>Geographic resolution</td><td><code>r=region</code></td></tr>
 <tr><td><code>m</code></td><td>Phylogeny x-axis measure</td><td><code>m=div</code></td></tr>
 <tr><td><code>l</code></td><td>Phylogeny layout</td><td><code>l=clock</code></td></tr>
+<tr><td><code>lang</code></td><td>Language</td><td><code>lang=ja</code> (Japanese)</td></tr>
 <tr><td><code>dmin</code></td><td>Temporal range (minimum)</td><td><code>dmin=2008-05-13</code></td></tr>
 <tr><td><code>dmax</code></td><td>Temporal range (maximum)</td><td><code>dmax=2010-05-13</code></td></tr>
 <tr><td><code>f_&lt;name&gt;</code></td><td>Data filter. Multiple values per key are <code>,</code> separated.</td><td><code>f_region=Oceania</code></td></tr>
@@ -129,4 +130,4 @@ <h2><a class="anchor" aria-hidden="true" id="url-query-options"></a><a href="#ur
 </table>
 <p><strong>See this in action:</strong></p>
 <p>For instance, go to <a href="https://nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;p=grid&amp;r=region">nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;r=region</a> and you'll see how we've changed the coloring to a temporal scale (<code>c=num_date</code>), we're only showing the tree &amp; map panels (<code>d=tree,map</code>), the tree x-axis is divergence (<code>m=div</code>) and the map resolution is region (<code>r=region</code>).</p>
-</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/27/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev">← </span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
\ No newline at end of file
+</span></div></article></div><div class="docLastUpdate"><em>Last updated on 4/8/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev">← </span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
\ No newline at end of file
diff --git a/docs/advanced-functionality/view-settings/index.html b/docs/advanced-functionality/view-settings/index.html
index 1e0ec5d65..e217390cc 100644
--- a/docs/advanced-functionality/view-settings/index.html
+++ b/docs/advanced-functionality/view-settings/index.html
@@ -109,6 +109,7 @@ <h2><a class="anchor" aria-hidden="true" id="url-query-options"></a><a href="#ur
 <tr><td><code>r</code></td><td>Geographic resolution</td><td><code>r=region</code></td></tr>
 <tr><td><code>m</code></td><td>Phylogeny x-axis measure</td><td><code>m=div</code></td></tr>
 <tr><td><code>l</code></td><td>Phylogeny layout</td><td><code>l=clock</code></td></tr>
+<tr><td><code>lang</code></td><td>Language</td><td><code>lang=ja</code> (Japanese)</td></tr>
 <tr><td><code>dmin</code></td><td>Temporal range (minimum)</td><td><code>dmin=2008-05-13</code></td></tr>
 <tr><td><code>dmax</code></td><td>Temporal range (maximum)</td><td><code>dmax=2010-05-13</code></td></tr>
 <tr><td><code>f_&lt;name&gt;</code></td><td>Data filter. Multiple values per key are <code>,</code> separated.</td><td><code>f_region=Oceania</code></td></tr>
@@ -129,4 +130,4 @@ <h2><a class="anchor" aria-hidden="true" id="url-query-options"></a><a href="#ur
 </table>
 <p><strong>See this in action:</strong></p>
 <p>For instance, go to <a href="https://nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;p=grid&amp;r=region">nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&amp;d=tree,map&amp;m=div&amp;r=region</a> and you'll see how we've changed the coloring to a temporal scale (<code>c=num_date</code>), we're only showing the tree &amp; map panels (<code>d=tree,map</code>), the tree x-axis is divergence (<code>m=div</code>) and the map resolution is region (<code>r=region</code>).</p>
-</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/27/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev">← </span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
\ No newline at end of file
+</span></div></article></div><div class="docLastUpdate"><em>Last updated on 4/8/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/advanced-functionality/second-trees"><span class="arrow-prev">← </span><span>Displaying multiple trees</span></a><a class="docs-next button" href="/auspice/advanced-functionality/drag-drop-csv-tsv"><span>Adding extra metadata via CSV/TSV</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#auspice-hardcoded-defaults">Auspice (hardcoded) defaults</a></li><li><a href="#dataset-json-configurable-defaults">Dataset (JSON) configurable defaults</a></li><li><a href="#url-query-options">URL query options</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
\ No newline at end of file
diff --git a/docs/contributing/overview.html b/docs/contributing/overview.html
index bbce04660..42902eea4 100644
--- a/docs/contributing/overview.html
+++ b/docs/contributing/overview.html
@@ -61,8 +61,12 @@
 <p>This project strictly adheres to the <a href="https://github.com/nextstrain/.github/blob/master/CODE_OF_CONDUCT.md">Contributor Covenant Code of Conduct</a>.</p>
 <p>Please see the <a href="https://github.com/orgs/nextstrain/projects">project boards</a> for currently available issues.</p>
 <h2><a class="anchor" aria-hidden="true" id="contributing-code"></a><a href="#contributing-code" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Contributing code</h2>
-<p><a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice locally.</p>
-<p>For pull requests, please use <a href="https://eslint.org/">eslint</a> as much as possible (via <code>npm run lint</code>).</p>
+<p>Code contributions are welcomed! <a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice from source.</p>
+<p>Please comment on an open issue if you are working on it.
+For changes unrelated to an open issue, please make an issue outlining what you would like to change/add.</p>
+<p>Please ensure there are no <strong>linting</strong> errors by running <code>npm run lint</code> (which uses <a href="https://eslint.org/">eslint</a>).
+In the future we will make this a requirement for PRs or commits.</p>
+<p>Where possible, <strong>please rebase</strong> your work onto master rather than merging changes from master into your PR.</p>
 <h2><a class="anchor" aria-hidden="true" id="contributing-to-documentation"></a><a href="#contributing-to-documentation" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Contributing to Documentation</h2>
 <p>Nextstrain documentation is available at <a href="https://nextstrain.github.io/auspice/">nextstrain.github.io/auspice/</a>.</p>
 <p>This documentation is built from files contained within the Auspice GitHub repo -- see the <a href="https://github.com/nextstrain/auspice/tree/master/docs-src">docs-src/README</a> within the <code>docs-src</code> directory for more details and instructions on how to contribute.</p>
diff --git a/docs/contributing/overview/index.html b/docs/contributing/overview/index.html
index bbce04660..42902eea4 100644
--- a/docs/contributing/overview/index.html
+++ b/docs/contributing/overview/index.html
@@ -61,8 +61,12 @@
 <p>This project strictly adheres to the <a href="https://github.com/nextstrain/.github/blob/master/CODE_OF_CONDUCT.md">Contributor Covenant Code of Conduct</a>.</p>
 <p>Please see the <a href="https://github.com/orgs/nextstrain/projects">project boards</a> for currently available issues.</p>
 <h2><a class="anchor" aria-hidden="true" id="contributing-code"></a><a href="#contributing-code" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Contributing code</h2>
-<p><a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice locally.</p>
-<p>For pull requests, please use <a href="https://eslint.org/">eslint</a> as much as possible (via <code>npm run lint</code>).</p>
+<p>Code contributions are welcomed! <a href="https://nextstrain.github.io/auspice/introduction/install">Please see the main auspice docs</a> for details on how to install and run auspice from source.</p>
+<p>Please comment on an open issue if you are working on it.
+For changes unrelated to an open issue, please make an issue outlining what you would like to change/add.</p>
+<p>Please ensure there are no <strong>linting</strong> errors by running <code>npm run lint</code> (which uses <a href="https://eslint.org/">eslint</a>).
+In the future we will make this a requirement for PRs or commits.</p>
+<p>Where possible, <strong>please rebase</strong> your work onto master rather than merging changes from master into your PR.</p>
 <h2><a class="anchor" aria-hidden="true" id="contributing-to-documentation"></a><a href="#contributing-to-documentation" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Contributing to Documentation</h2>
 <p>Nextstrain documentation is available at <a href="https://nextstrain.github.io/auspice/">nextstrain.github.io/auspice/</a>.</p>
 <p>This documentation is built from files contained within the Auspice GitHub repo -- see the <a href="https://github.com/nextstrain/auspice/tree/master/docs-src">docs-src/README</a> within the <code>docs-src</code> directory for more details and instructions on how to contribute.</p>
diff --git a/docs/releases/changelog.html b/docs/releases/changelog.html
index a65af9bfb..06d7956bc 100644
--- a/docs/releases/changelog.html
+++ b/docs/releases/changelog.html
@@ -1,4 +1,4 @@
-<!DOCTYPE html><html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Changelog · Auspice</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="## version 2.11.1 - 2020/03/28"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Changelog · Auspice"/><meta property="og:type" content="website"/><meta property="og:url" content="https://nextstrain.github.io/auspice/"/><meta property="og:description" content="## version 2.11.1 - 2020/03/28"/><meta property="og:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><meta name="twitter:card" content="summary"/><meta name="twitter:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><link rel="shortcut icon" href="/auspice/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/solarized-dark.min.css"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><script src="/auspice/js/scrollSpy.js"></script><link rel="stylesheet" href="/auspice/css/main.css"/><script src="/auspice/js/codetabs.js"></script></head><body class="sideNavVisible separateOnPageNav"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/auspice/"><img class="logo" src="/auspice/img/logo-light.svg" alt="Auspice"/><h2 class="headerTitleWithLogo">Auspice</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class="siteNavGroupActive"><a href="/auspice/introduction/overview" target="_self">Docs</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><div class="hamburger-menu"><div class="line1"></div><div class="line2"></div><div class="line3"></div></div></div><h2><i>›</i><span>Release Notes</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">Introduction</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/introduction/overview">Overview</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/install">Install Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/how-to-run">How to Run Auspice</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Advanced Functionality</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/second-trees">Displaying multiple trees</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/view-settings">View Settings</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/drag-drop-csv-tsv">Adding extra metadata via CSV/TSV</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/misc">Miscellaneous</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Customising Auspice</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/customise-client/introduction">Customising Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/api">Client Customisation API</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/requests">Requests Made from the Client</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Using a Custom Server</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/server/introduction">Auspice servers</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/api">Server API</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/authentication">Authentication</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Narratives</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/narratives/introduction">Communicating Results Using Narratives</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/how-to-write">Writing a Narrative</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/create-pdf">Converting a narrative to PDF</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Release Notes</h3><ul class=""><li class="navListItem navListItemActive"><a class="navItem" href="/auspice/releases/changelog">Changelog</a></li><li class="navListItem"><a class="navItem" href="/auspice/releases/v2">Auspice Version 2.0</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Contributing</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/contributing/overview">Contributing to Auspice development</a></li></ul></div></div></section></div><script>
+<!DOCTYPE html><html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Changelog · Auspice</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="## version 2.12.0 - 2020/04/08"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Changelog · Auspice"/><meta property="og:type" content="website"/><meta property="og:url" content="https://nextstrain.github.io/auspice/"/><meta property="og:description" content="## version 2.12.0 - 2020/04/08"/><meta property="og:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><meta name="twitter:card" content="summary"/><meta name="twitter:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><link rel="shortcut icon" href="/auspice/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/solarized-dark.min.css"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><script src="/auspice/js/scrollSpy.js"></script><link rel="stylesheet" href="/auspice/css/main.css"/><script src="/auspice/js/codetabs.js"></script></head><body class="sideNavVisible separateOnPageNav"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/auspice/"><img class="logo" src="/auspice/img/logo-light.svg" alt="Auspice"/><h2 class="headerTitleWithLogo">Auspice</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class="siteNavGroupActive"><a href="/auspice/introduction/overview" target="_self">Docs</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><div class="hamburger-menu"><div class="line1"></div><div class="line2"></div><div class="line3"></div></div></div><h2><i>›</i><span>Release Notes</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">Introduction</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/introduction/overview">Overview</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/install">Install Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/how-to-run">How to Run Auspice</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Advanced Functionality</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/second-trees">Displaying multiple trees</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/view-settings">View Settings</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/drag-drop-csv-tsv">Adding extra metadata via CSV/TSV</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/misc">Miscellaneous</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Customising Auspice</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/customise-client/introduction">Customising Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/api">Client Customisation API</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/requests">Requests Made from the Client</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Using a Custom Server</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/server/introduction">Auspice servers</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/api">Server API</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/authentication">Authentication</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Narratives</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/narratives/introduction">Communicating Results Using Narratives</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/how-to-write">Writing a Narrative</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/create-pdf">Converting a narrative to PDF</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Release Notes</h3><ul class=""><li class="navListItem navListItemActive"><a class="navItem" href="/auspice/releases/changelog">Changelog</a></li><li class="navListItem"><a class="navItem" href="/auspice/releases/v2">Auspice Version 2.0</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Contributing</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/contributing/overview">Contributing to Auspice development</a></li></ul></div></div></section></div><script>
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+        </script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Changelog</h1></header><article><div><span><h2><a class="anchor" aria-hidden="true" id="version-2120-2020-04-08"></a><a href="#version-2120-2020-04-08" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.12.0 - 2020/04/08</h2>
+<ul>
+<li>Add a legend to the map! <a href="https://github.com/nextstrain/auspice/pull/935">See PR 935</a></li>
+<li>Improve the animation smoothness, especially for datasets with limited temporal range. <a href="https://github.com/nextstrain/auspice/pull/920">See PR 920</a></li>
+<li>Add Japanese translation <a href="https://github.com/nextstrain/auspice/pull/1045">See PR 1045</a></li>
+<li>Reinstate the <code>lang</code> URL query to allow the URL to choose the language.</li>
+<li>Remove unnecessary lodash code from the bundles. <a href="https://github.com/nextstrain/auspice/pull/1018">See PR 1018</a></li>
+<li>Update how the <code>Root</code> component is imported. <a href="https://github.com/nextstrain/auspice/pull/1029">See PR 1029</a></li>
+<li>Fix errors in the sizing of the map buttons. <a href="https://github.com/nextstrain/auspice/pull/1040">See PR 1040</a></li>
+<li>Improve rendering of tree tip labels by only counting the selected (visible) tips. <a href="https://github.com/nextstrain/auspice/pull/1043">See PR 1043</a></li>
+</ul>
+<h2><a class="anchor" aria-hidden="true" id="version-2114-2020-04-04"></a><a href="#version-2114-2020-04-04" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.11.4 - 2020/04/04</h2>
+<ul>
+<li>Temporarily remove SVG gradients in the tree due to bugs in multiple browsers. <a href="https://github.com/nextstrain/auspice/pull/1042">See PR 1042</a></li>
+</ul>
+<h2><a class="anchor" aria-hidden="true" id="version-2113-2020-04-02"></a><a href="#version-2113-2020-04-02" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.11.3 - 2020/04/02</h2>
+<ul>
+<li>Add Portuguese translation. <a href="https://github.com/nextstrain/auspice/pull/1017">See PR 1017</a></li>
+<li>Fig bug where some branches would not display on certain browsers. <a href="https://github.com/nextstrain/auspice/pull/1022">See PR 1022</a></li>
+<li>Fix bug with selected dates shown when no genomes were selected. <a href="https://github.com/nextstrain/auspice/pull/1011">See PR 1011</a></li>
+<li>Show <code>--includeTiming</code> argument when viewing help (<code>--help</code>).</li>
+<li>Add second node version to TravisCI.  <a href="https://github.com/nextstrain/auspice/pull/1023">See PR 1023</a></li>
+<li>Fix docs typo. <a href="https://github.com/nextstrain/auspice/pull/1027">See PR 1027</a></li>
+</ul>
+<h2><a class="anchor" aria-hidden="true" id="version-2112-2020-03-30"></a><a href="#version-2112-2020-03-30" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.11.2 - 2020/03/30</h2>
+<ul>
+<li>Add French translation - <a href="https://github.com/nextstrain/auspice/pull/1020">See PR 1020</a></li>
+<li>Improve rendering of long strain names in strain search - <a href="https://github.com/nextstrain/auspice/pull/1026">See PR 1026</a></li>
+<li>Lithuanian translation fixes</li>
+</ul>
+<h2><a class="anchor" aria-hidden="true" id="version-2111-2020-03-28"></a><a href="#version-2111-2020-03-28" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.11.1 - 2020/03/28</h2>
 <ul>
 <li>Add Lithuanian translation</li>
 <li>Fig bugs in translation strings which contained <code>:</code> or <code>.</code></li>
@@ -960,4 +990,4 @@ <h2><a class="anchor" aria-hidden="true" id="version-171-2017-10-31"></a><a href
 </ul>
 <h2><a class="anchor" aria-hidden="true" id="version-170-2017-10-17"></a><a href="#version-170-2017-10-17" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 1.7.0 - 2017/10/17</h2>
 <h2><a class="anchor" aria-hidden="true" id="version-2018-01-18"></a><a href="#version-2018-01-18" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version  - 2018/01/18</h2>
-</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/create-pdf"><span class="arrow-prev">← </span><span>Converting a narrative to PDF</span></a><a class="docs-next button" href="/auspice/releases/v2"><span>Auspice Version 2.0</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#version-2111-2020-03-28">version 2.11.1 - 2020/03/28</a></li><li><a href="#version-2110-2020-03-27">version 2.11.0 - 2020/03/27</a></li><li><a href="#version-2100-2020-03-24">version 2.10.0 - 2020/03/24</a></li><li><a href="#version-291-2020-03-23">version 2.9.1 - 2020/03/23</a></li><li><a href="#version-290-2020-03-23">version 2.9.0 - 2020/03/23</a></li><li><a href="#version-281-2020-03-20">version 2.8.1 - 2020/03/20</a></li><li><a href="#version-280-2020-03-20">version 2.8.0 - 2020/03/20</a></li><li><a href="#version-270-2020-03-15">version 2.7.0 - 2020/03/15</a></li><li><a href="#version-260-2020-03-09">version 2.6.0 - 2020/03/09</a></li><li><a href="#version-257-2020-03-09">version 2.5.7 - 2020/03/09</a></li><li><a href="#version-256-2020-03-09">version 2.5.6 - 2020/03/09</a></li><li><a href="#version-255-2020-03-04">version 2.5.5 - 2020/03/04</a></li><li><a href="#version-254-2020-02-26">version 2.5.4 - 2020/02/26</a></li><li><a href="#version-253-2020-02-12">version 2.5.3 - 2020/02/12</a></li><li><a href="#version-252-2020-02-11">version 2.5.2 - 2020/02/11</a></li><li><a href="#version-251-2020-02-07">version 2.5.1 - 2020/02/07</a></li><li><a href="#version-250-2020-02-05">version 2.5.0 - 2020/02/05</a></li><li><a href="#version-241-2020-02-01">version 2.4.1 - 2020/02/01</a></li><li><a href="#version-240-2020-01-31">version 2.4.0 - 2020/01/31</a></li><li><a href="#version-237-2020-01-30">version 2.3.7 - 2020/01/30</a></li><li><a href="#version-236-2020-01-30">version 2.3.6 - 2020/01/30</a></li><li><a href="#version-235-2020-01-28">version 2.3.5 - 2020/01/28</a></li><li><a href="#version-234-2020-01-28">version 2.3.4 - 2020/01/28</a></li><li><a href="#version-233-2020-01-27">version 2.3.3 - 2020/01/27</a></li><li><a href="#version-232-2020-01-24">version 2.3.2 - 2020/01/24</a></li><li><a href="#version-231-2020-01-24">version 2.3.1 - 2020/01/24</a></li><li><a href="#version-230-2020-01-23">version 2.3.0 - 2020/01/23</a></li><li><a href="#version-224-2020-01-11">version 2.2.4 - 2020/01/11</a></li><li><a href="#version-223-2020-01-06">version 2.2.3 - 2020/01/06</a></li><li><a href="#version-222-2020-01-03">version 2.2.2 - 2020/01/03</a></li><li><a href="#version-221-2020-01-03">version 2.2.1 - 2020/01/03</a></li><li><a href="#version-220-2019-12-16">version 2.2.0 - 2019/12/16</a></li><li><a href="#version-210-2019-11-15">version 2.1.0 - 2019/11/15</a></li><li><a href="#version-203-2019-11-06">version 2.0.3 - 2019/11/06</a></li><li><a href="#version-202-2019-10-30">version 2.0.2 - 2019/10/30</a></li><li><a href="#version-201-2019-10-25">version 2.0.1 - 2019/10/25</a></li><li><a href="#version-200-2019-10-21">version 2.0.0 - 2019/10/21</a></li><li><a href="#version-1391-2019-10-21">version 1.39.1 - 2019/10/21</a></li><li><a href="#version-1390-2019-09-12">version 1.39.0 - 2019/09/12</a></li><li><a href="#version-1382-2019-09-06">version 1.38.2 - 2019/09/06</a></li><li><a href="#version-1381-2019-09-06">version 1.38.1 - 2019/09/06</a></li><li><a href="#version-1380-2019-08-29">version 1.38.0 - 2019/08/29</a></li><li><a href="#version-1375-2019-08-09">version 1.37.5 - 2019/08/09</a></li><li><a href="#version-1374-2019-08-04">version 1.37.4 - 2019/08/04</a></li><li><a href="#version-1373-2019-07-29">version 1.37.3 - 2019/07/29</a></li><li><a href="#version-1372-2019-07-20">version 1.37.2 - 2019/07/20</a></li><li><a href="#version-1371-2019-07-13">version 1.37.1 - 2019/07/13</a></li><li><a href="#version-1370-2019-07-09">version 1.37.0 - 2019/07/09</a></li><li><a href="#version-1366-2019-05-18">version 1.36.6 - 2019/05/18</a></li><li><a href="#version-1365-2019-04-17">version 1.36.5 - 2019/04/17</a></li><li><a href="#version-1364-2019-03-16">version 1.36.4 - 2019/03/16</a></li><li><a href="#version-1363-2019-03-11">version 1.36.3 - 2019/03/11</a></li><li><a href="#version-1362-2019-03-04">version 1.36.2 - 2019/03/04</a></li><li><a href="#version-1361-2019-02-27">version 1.36.1 - 2019/02/27</a></li><li><a href="#version-1360-2019-02-25">version 1.36.0 - 2019/02/25</a></li><li><a href="#version-1355-2019-02-08">version 1.35.5 - 2019/02/08</a></li><li><a href="#version-1354-2019-01-28">version 1.35.4 - 2019/01/28</a></li><li><a href="#version-1353-2019-01-25">version 1.35.3 - 2019/01/25</a></li><li><a href="#version-1352-2019-01-16">version 1.35.2 - 2019/01/16</a></li><li><a href="#version-1344-2019-01-15">version 1.34.4 - 2019/01/15</a></li><li><a href="#version-1343-2018-12-18">version 1.34.3 - 2018/12/18</a></li><li><a href="#version-1342-2018-12-05">version 1.34.2 - 2018/12/05</a></li><li><a href="#version-1341-2018-11-29">version 1.34.1 - 2018/11/29</a></li><li><a href="#version-1340-2018-11-19">version 1.34.0 - 2018/11/19</a></li><li><a href="#version-1330-2018-11-18">version 1.33.0 - 2018/11/18</a></li><li><a href="#version-1320-2018-11-02">version 1.32.0 - 2018/11/02</a></li><li><a href="#version-1310-2018-10-29">version 1.31.0 - 2018/10/29</a></li><li><a href="#version-1303-2018-09-19">version 1.30.3 - 2018/09/19</a></li><li><a href="#version-1302-2018-09-07">version 1.30.2 - 2018/09/07</a></li><li><a href="#version-1301-2018-09-05">version 1.30.1 - 2018/09/05</a></li><li><a href="#version-1300-2018-09-05">version 1.30.0 - 2018/09/05</a></li><li><a href="#version-1290-2018-08-31">version 1.29.0 - 2018/08/31</a><ul class="toc-headings"><li><a href="#narrative-improvements">Narrative improvements</a></li></ul></li><li><a href="#version-1280-2018-08-25">version 1.28.0 - 2018/08/25</a></li><li><a href="#version-1271-2018-08-24">version 1.27.1 - 2018/08/24</a></li><li><a href="#version-1270-2018-08-20">version 1.27.0 - 2018/08/20</a></li><li><a href="#version-1260-2018-08-20">version 1.26.0 - 2018/08/20</a></li><li><a href="#version-1252-2018-08-17">version 1.25.2 - 2018/08/17</a></li><li><a href="#version-1251-2018-08-10">version 1.25.1 - 2018/08/10</a></li><li><a href="#version-1250-2018-08-09">version 1.25.0 - 2018/08/09</a></li><li><a href="#version-1241-2018-08-08">version 1.24.1 - 2018/08/08</a></li><li><a href="#version-1240-2018-08-05">version 1.24.0 - 2018/08/05</a></li><li><a href="#version-1232-2018-07-30">version 1.23.2 - 2018/07/30</a></li><li><a href="#version-1231-2018-07-30">version 1.23.1 - 2018/07/30</a></li><li><a href="#version-1230-2018-07-28">version 1.23.0 - 2018/07/28</a></li><li><a href="#version-1223-2018-07-19">version 1.22.3 - 2018/07/19</a></li><li><a href="#version-1222-2018-07-10">version 1.22.2 - 2018/07/10</a></li><li><a href="#version-1221-2018-07-09">version 1.22.1 - 2018/07/09</a></li><li><a href="#version-1220-2018-07-03">version 1.22.0 - 2018/07/03</a></li><li><a href="#version-1213-2018-06-27">version 1.21.3 - 2018/06/27</a></li><li><a href="#version-1212-2018-06-07">version 1.21.2 - 2018/06/07</a></li><li><a href="#version-1211-2018-06-04">version 1.21.1 - 2018/06/04</a></li><li><a href="#version-1210-2018-06-01">version 1.21.0 - 2018/06/01</a></li><li><a href="#version-1203-2018-05-30">version 1.20.3 - 2018/05/30</a></li><li><a href="#version-1202-2018-05-21">version 1.20.2 - 2018/05/21</a></li><li><a href="#version-1201-2018-05-21">version 1.20.1 - 2018/05/21</a></li><li><a href="#version-1200-2018-05-15">version 1.20.0 - 2018/05/15</a></li><li><a href="#version-1191-2018-05-09">version 1.19.1 - 2018/05/09</a></li><li><a href="#version-1190-2018-05-09">version 1.19.0 - 2018/05/09</a></li><li><a href="#version-11810-2018-05-07">version 1.18.10 - 2018/05/07</a></li><li><a href="#version-1189-2018-05-03">version 1.18.9 - 2018/05/03</a></li><li><a href="#version-1188-2018-05-02">version 1.18.8 - 2018/05/02</a></li><li><a href="#version-1187-2018-05-02">version 1.18.7 - 2018/05/02</a></li><li><a href="#version-1186-2018-04-30">version 1.18.6 - 2018/04/30</a></li><li><a href="#version-1185-2018-04-27">version 1.18.5 - 2018/04/27</a></li><li><a href="#version-1184-2018-04-26">version 1.18.4 - 2018/04/26</a></li><li><a href="#version-1183-2018-04-23">version 1.18.3 - 2018/04/23</a></li><li><a href="#version-1182-2018-04-16">version 1.18.2 - 2018/04/16</a></li><li><a href="#version-1181-2018-04-15">version 1.18.1 - 2018/04/15</a></li><li><a href="#version-1180-2018-04-14">version 1.18.0 - 2018/04/14</a></li><li><a href="#version-1174-2018-04-10">version 1.17.4 - 2018/04/10</a></li><li><a href="#version-1173-2018-04-04">version 1.17.3 - 2018/04/04</a></li><li><a href="#version-1172-2018-04-02">version 1.17.2 - 2018/04/02</a></li><li><a href="#version-1171-2018-03-28">version 1.17.1 - 2018/03/28</a></li><li><a href="#version-1170-2018-03-26">version 1.17.0 - 2018/03/26</a></li><li><a href="#version-1165-2018-03-26">version 1.16.5 - 2018/03/26</a></li><li><a href="#version-1164-2018-03-22">version 1.16.4 - 2018/03/22</a></li><li><a href="#version-1163-2018-03-21">version 1.16.3 - 2018/03/21</a></li><li><a href="#version-1162-2018-03-21">version 1.16.2 - 2018/03/21</a></li><li><a href="#version-1161-2018-03-16">version 1.16.1 - 2018/03/16</a></li><li><a href="#version-1160-2018-03-16">version 1.16.0 - 2018/03/16</a><ul class="toc-headings"><li><a href="#browser-support">Browser support</a></li></ul></li><li><a href="#version-1151-2018-03-14">version 1.15.1 - 2018/03/14</a></li><li><a href="#version-1150-2018-03-12">version 1.15.0 - 2018/03/12</a></li><li><a href="#version-1144-2018-03-05">version 1.14.4 - 2018/03/05</a></li><li><a href="#version-1143-2018-03-01">version 1.14.3 - 2018/03/01</a></li><li><a href="#version-1142-2018-02-28">version 1.14.2 - 2018/02/28</a></li><li><a href="#version-1141-2018-02-27">version 1.14.1 - 2018/02/27</a></li><li><a href="#version-1140-2018-02-27">version 1.14.0 - 2018/02/27</a><ul class="toc-headings"><li><a href="#features">Features</a></li><li><a href="#internals-1">Internals</a></li></ul></li><li><a href="#version-1132-2018-02-26">version 1.13.2 - 2018/02/26</a></li><li><a href="#version-1131-2018-02-26">version 1.13.1 - 2018/02/26</a></li><li><a href="#version-1130-2018-02-26">version 1.13.0 - 2018/02/26</a><ul class="toc-headings"><li><a href="#features-1">Features</a></li><li><a href="#internals-2">Internals</a></li></ul></li><li><a href="#version-1120-2018-02-14">version 1.12.0 - 2018/02/14</a><ul class="toc-headings"><li><a href="#features-2">Features</a></li><li><a href="#internals-3">Internals</a></li></ul></li><li><a href="#version-1110-2018-02-05">version 1.11.0 - 2018/02/05</a><ul class="toc-headings"><li><a href="#features-3">Features</a></li><li><a href="#internals-4">Internals</a></li></ul></li><li><a href="#version-1100-2018-02-05">version 1.10.0 - 2018/02/05</a><ul class="toc-headings"><li><a href="#features-4">Features</a></li><li><a href="#internals-5">Internals</a></li></ul></li><li><a href="#version-190-2018-01-30">version 1.9.0 - 2018/01/30</a><ul class="toc-headings"><li><a href="#animation">Animation</a></li><li><a href="#misc">misc</a></li></ul></li><li><a href="#version-180-2018-01-18">version 1.8.0 - 2018/01/18</a></li><li><a href="#version-172-2018-1-4">version 1.7.2 - 2018/1/4</a></li><li><a href="#version-171-2017-10-31">version 1.7.1 - 2017/10/31</a></li><li><a href="#version-170-2017-10-17">version 1.7.0 - 2017/10/17</a></li><li><a href="#version-2018-01-18">version  - 2018/01/18</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
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+</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/create-pdf"><span class="arrow-prev">← </span><span>Converting a narrative to PDF</span></a><a class="docs-next button" href="/auspice/releases/v2"><span>Auspice Version 2.0</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#version-2120-2020-04-08">version 2.12.0 - 2020/04/08</a></li><li><a href="#version-2114-2020-04-04">version 2.11.4 - 2020/04/04</a></li><li><a href="#version-2113-2020-04-02">version 2.11.3 - 2020/04/02</a></li><li><a href="#version-2112-2020-03-30">version 2.11.2 - 2020/03/30</a></li><li><a href="#version-2111-2020-03-28">version 2.11.1 - 2020/03/28</a></li><li><a href="#version-2110-2020-03-27">version 2.11.0 - 2020/03/27</a></li><li><a href="#version-2100-2020-03-24">version 2.10.0 - 2020/03/24</a></li><li><a href="#version-291-2020-03-23">version 2.9.1 - 2020/03/23</a></li><li><a href="#version-290-2020-03-23">version 2.9.0 - 2020/03/23</a></li><li><a href="#version-281-2020-03-20">version 2.8.1 - 2020/03/20</a></li><li><a href="#version-280-2020-03-20">version 2.8.0 - 2020/03/20</a></li><li><a href="#version-270-2020-03-15">version 2.7.0 - 2020/03/15</a></li><li><a href="#version-260-2020-03-09">version 2.6.0 - 2020/03/09</a></li><li><a href="#version-257-2020-03-09">version 2.5.7 - 2020/03/09</a></li><li><a href="#version-256-2020-03-09">version 2.5.6 - 2020/03/09</a></li><li><a href="#version-255-2020-03-04">version 2.5.5 - 2020/03/04</a></li><li><a href="#version-254-2020-02-26">version 2.5.4 - 2020/02/26</a></li><li><a href="#version-253-2020-02-12">version 2.5.3 - 2020/02/12</a></li><li><a href="#version-252-2020-02-11">version 2.5.2 - 2020/02/11</a></li><li><a href="#version-251-2020-02-07">version 2.5.1 - 2020/02/07</a></li><li><a href="#version-250-2020-02-05">version 2.5.0 - 2020/02/05</a></li><li><a href="#version-241-2020-02-01">version 2.4.1 - 2020/02/01</a></li><li><a href="#version-240-2020-01-31">version 2.4.0 - 2020/01/31</a></li><li><a href="#version-237-2020-01-30">version 2.3.7 - 2020/01/30</a></li><li><a href="#version-236-2020-01-30">version 2.3.6 - 2020/01/30</a></li><li><a href="#version-235-2020-01-28">version 2.3.5 - 2020/01/28</a></li><li><a href="#version-234-2020-01-28">version 2.3.4 - 2020/01/28</a></li><li><a href="#version-233-2020-01-27">version 2.3.3 - 2020/01/27</a></li><li><a href="#version-232-2020-01-24">version 2.3.2 - 2020/01/24</a></li><li><a href="#version-231-2020-01-24">version 2.3.1 - 2020/01/24</a></li><li><a href="#version-230-2020-01-23">version 2.3.0 - 2020/01/23</a></li><li><a href="#version-224-2020-01-11">version 2.2.4 - 2020/01/11</a></li><li><a href="#version-223-2020-01-06">version 2.2.3 - 2020/01/06</a></li><li><a href="#version-222-2020-01-03">version 2.2.2 - 2020/01/03</a></li><li><a href="#version-221-2020-01-03">version 2.2.1 - 2020/01/03</a></li><li><a href="#version-220-2019-12-16">version 2.2.0 - 2019/12/16</a></li><li><a href="#version-210-2019-11-15">version 2.1.0 - 2019/11/15</a></li><li><a href="#version-203-2019-11-06">version 2.0.3 - 2019/11/06</a></li><li><a href="#version-202-2019-10-30">version 2.0.2 - 2019/10/30</a></li><li><a href="#version-201-2019-10-25">version 2.0.1 - 2019/10/25</a></li><li><a href="#version-200-2019-10-21">version 2.0.0 - 2019/10/21</a></li><li><a href="#version-1391-2019-10-21">version 1.39.1 - 2019/10/21</a></li><li><a href="#version-1390-2019-09-12">version 1.39.0 - 2019/09/12</a></li><li><a href="#version-1382-2019-09-06">version 1.38.2 - 2019/09/06</a></li><li><a href="#version-1381-2019-09-06">version 1.38.1 - 2019/09/06</a></li><li><a href="#version-1380-2019-08-29">version 1.38.0 - 2019/08/29</a></li><li><a href="#version-1375-2019-08-09">version 1.37.5 - 2019/08/09</a></li><li><a href="#version-1374-2019-08-04">version 1.37.4 - 2019/08/04</a></li><li><a href="#version-1373-2019-07-29">version 1.37.3 - 2019/07/29</a></li><li><a href="#version-1372-2019-07-20">version 1.37.2 - 2019/07/20</a></li><li><a href="#version-1371-2019-07-13">version 1.37.1 - 2019/07/13</a></li><li><a href="#version-1370-2019-07-09">version 1.37.0 - 2019/07/09</a></li><li><a href="#version-1366-2019-05-18">version 1.36.6 - 2019/05/18</a></li><li><a href="#version-1365-2019-04-17">version 1.36.5 - 2019/04/17</a></li><li><a href="#version-1364-2019-03-16">version 1.36.4 - 2019/03/16</a></li><li><a href="#version-1363-2019-03-11">version 1.36.3 - 2019/03/11</a></li><li><a href="#version-1362-2019-03-04">version 1.36.2 - 2019/03/04</a></li><li><a href="#version-1361-2019-02-27">version 1.36.1 - 2019/02/27</a></li><li><a href="#version-1360-2019-02-25">version 1.36.0 - 2019/02/25</a></li><li><a href="#version-1355-2019-02-08">version 1.35.5 - 2019/02/08</a></li><li><a href="#version-1354-2019-01-28">version 1.35.4 - 2019/01/28</a></li><li><a href="#version-1353-2019-01-25">version 1.35.3 - 2019/01/25</a></li><li><a href="#version-1352-2019-01-16">version 1.35.2 - 2019/01/16</a></li><li><a href="#version-1344-2019-01-15">version 1.34.4 - 2019/01/15</a></li><li><a href="#version-1343-2018-12-18">version 1.34.3 - 2018/12/18</a></li><li><a href="#version-1342-2018-12-05">version 1.34.2 - 2018/12/05</a></li><li><a href="#version-1341-2018-11-29">version 1.34.1 - 2018/11/29</a></li><li><a href="#version-1340-2018-11-19">version 1.34.0 - 2018/11/19</a></li><li><a href="#version-1330-2018-11-18">version 1.33.0 - 2018/11/18</a></li><li><a href="#version-1320-2018-11-02">version 1.32.0 - 2018/11/02</a></li><li><a href="#version-1310-2018-10-29">version 1.31.0 - 2018/10/29</a></li><li><a href="#version-1303-2018-09-19">version 1.30.3 - 2018/09/19</a></li><li><a href="#version-1302-2018-09-07">version 1.30.2 - 2018/09/07</a></li><li><a href="#version-1301-2018-09-05">version 1.30.1 - 2018/09/05</a></li><li><a href="#version-1300-2018-09-05">version 1.30.0 - 2018/09/05</a></li><li><a href="#version-1290-2018-08-31">version 1.29.0 - 2018/08/31</a><ul class="toc-headings"><li><a href="#narrative-improvements">Narrative improvements</a></li></ul></li><li><a href="#version-1280-2018-08-25">version 1.28.0 - 2018/08/25</a></li><li><a href="#version-1271-2018-08-24">version 1.27.1 - 2018/08/24</a></li><li><a href="#version-1270-2018-08-20">version 1.27.0 - 2018/08/20</a></li><li><a href="#version-1260-2018-08-20">version 1.26.0 - 2018/08/20</a></li><li><a href="#version-1252-2018-08-17">version 1.25.2 - 2018/08/17</a></li><li><a href="#version-1251-2018-08-10">version 1.25.1 - 2018/08/10</a></li><li><a href="#version-1250-2018-08-09">version 1.25.0 - 2018/08/09</a></li><li><a href="#version-1241-2018-08-08">version 1.24.1 - 2018/08/08</a></li><li><a href="#version-1240-2018-08-05">version 1.24.0 - 2018/08/05</a></li><li><a href="#version-1232-2018-07-30">version 1.23.2 - 2018/07/30</a></li><li><a href="#version-1231-2018-07-30">version 1.23.1 - 2018/07/30</a></li><li><a href="#version-1230-2018-07-28">version 1.23.0 - 2018/07/28</a></li><li><a href="#version-1223-2018-07-19">version 1.22.3 - 2018/07/19</a></li><li><a href="#version-1222-2018-07-10">version 1.22.2 - 2018/07/10</a></li><li><a href="#version-1221-2018-07-09">version 1.22.1 - 2018/07/09</a></li><li><a href="#version-1220-2018-07-03">version 1.22.0 - 2018/07/03</a></li><li><a href="#version-1213-2018-06-27">version 1.21.3 - 2018/06/27</a></li><li><a href="#version-1212-2018-06-07">version 1.21.2 - 2018/06/07</a></li><li><a href="#version-1211-2018-06-04">version 1.21.1 - 2018/06/04</a></li><li><a href="#version-1210-2018-06-01">version 1.21.0 - 2018/06/01</a></li><li><a href="#version-1203-2018-05-30">version 1.20.3 - 2018/05/30</a></li><li><a href="#version-1202-2018-05-21">version 1.20.2 - 2018/05/21</a></li><li><a href="#version-1201-2018-05-21">version 1.20.1 - 2018/05/21</a></li><li><a href="#version-1200-2018-05-15">version 1.20.0 - 2018/05/15</a></li><li><a href="#version-1191-2018-05-09">version 1.19.1 - 2018/05/09</a></li><li><a href="#version-1190-2018-05-09">version 1.19.0 - 2018/05/09</a></li><li><a href="#version-11810-2018-05-07">version 1.18.10 - 2018/05/07</a></li><li><a href="#version-1189-2018-05-03">version 1.18.9 - 2018/05/03</a></li><li><a href="#version-1188-2018-05-02">version 1.18.8 - 2018/05/02</a></li><li><a href="#version-1187-2018-05-02">version 1.18.7 - 2018/05/02</a></li><li><a href="#version-1186-2018-04-30">version 1.18.6 - 2018/04/30</a></li><li><a href="#version-1185-2018-04-27">version 1.18.5 - 2018/04/27</a></li><li><a href="#version-1184-2018-04-26">version 1.18.4 - 2018/04/26</a></li><li><a href="#version-1183-2018-04-23">version 1.18.3 - 2018/04/23</a></li><li><a href="#version-1182-2018-04-16">version 1.18.2 - 2018/04/16</a></li><li><a href="#version-1181-2018-04-15">version 1.18.1 - 2018/04/15</a></li><li><a href="#version-1180-2018-04-14">version 1.18.0 - 2018/04/14</a></li><li><a href="#version-1174-2018-04-10">version 1.17.4 - 2018/04/10</a></li><li><a href="#version-1173-2018-04-04">version 1.17.3 - 2018/04/04</a></li><li><a href="#version-1172-2018-04-02">version 1.17.2 - 2018/04/02</a></li><li><a href="#version-1171-2018-03-28">version 1.17.1 - 2018/03/28</a></li><li><a href="#version-1170-2018-03-26">version 1.17.0 - 2018/03/26</a></li><li><a href="#version-1165-2018-03-26">version 1.16.5 - 2018/03/26</a></li><li><a href="#version-1164-2018-03-22">version 1.16.4 - 2018/03/22</a></li><li><a href="#version-1163-2018-03-21">version 1.16.3 - 2018/03/21</a></li><li><a href="#version-1162-2018-03-21">version 1.16.2 - 2018/03/21</a></li><li><a href="#version-1161-2018-03-16">version 1.16.1 - 2018/03/16</a></li><li><a href="#version-1160-2018-03-16">version 1.16.0 - 2018/03/16</a><ul class="toc-headings"><li><a href="#browser-support">Browser support</a></li></ul></li><li><a href="#version-1151-2018-03-14">version 1.15.1 - 2018/03/14</a></li><li><a href="#version-1150-2018-03-12">version 1.15.0 - 2018/03/12</a></li><li><a href="#version-1144-2018-03-05">version 1.14.4 - 2018/03/05</a></li><li><a href="#version-1143-2018-03-01">version 1.14.3 - 2018/03/01</a></li><li><a href="#version-1142-2018-02-28">version 1.14.2 - 2018/02/28</a></li><li><a href="#version-1141-2018-02-27">version 1.14.1 - 2018/02/27</a></li><li><a href="#version-1140-2018-02-27">version 1.14.0 - 2018/02/27</a><ul class="toc-headings"><li><a href="#features">Features</a></li><li><a href="#internals-1">Internals</a></li></ul></li><li><a href="#version-1132-2018-02-26">version 1.13.2 - 2018/02/26</a></li><li><a href="#version-1131-2018-02-26">version 1.13.1 - 2018/02/26</a></li><li><a href="#version-1130-2018-02-26">version 1.13.0 - 2018/02/26</a><ul class="toc-headings"><li><a href="#features-1">Features</a></li><li><a href="#internals-2">Internals</a></li></ul></li><li><a href="#version-1120-2018-02-14">version 1.12.0 - 2018/02/14</a><ul class="toc-headings"><li><a href="#features-2">Features</a></li><li><a href="#internals-3">Internals</a></li></ul></li><li><a href="#version-1110-2018-02-05">version 1.11.0 - 2018/02/05</a><ul class="toc-headings"><li><a href="#features-3">Features</a></li><li><a href="#internals-4">Internals</a></li></ul></li><li><a href="#version-1100-2018-02-05">version 1.10.0 - 2018/02/05</a><ul class="toc-headings"><li><a href="#features-4">Features</a></li><li><a href="#internals-5">Internals</a></li></ul></li><li><a href="#version-190-2018-01-30">version 1.9.0 - 2018/01/30</a><ul class="toc-headings"><li><a href="#animation">Animation</a></li><li><a href="#misc">misc</a></li></ul></li><li><a href="#version-180-2018-01-18">version 1.8.0 - 2018/01/18</a></li><li><a href="#version-172-2018-1-4">version 1.7.2 - 2018/1/4</a></li><li><a href="#version-171-2017-10-31">version 1.7.1 - 2017/10/31</a></li><li><a href="#version-170-2017-10-17">version 1.7.0 - 2017/10/17</a></li><li><a href="#version-2018-01-18">version  - 2018/01/18</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
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-<!DOCTYPE html><html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Changelog · Auspice</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="## version 2.11.1 - 2020/03/28"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Changelog · Auspice"/><meta property="og:type" content="website"/><meta property="og:url" content="https://nextstrain.github.io/auspice/"/><meta property="og:description" content="## version 2.11.1 - 2020/03/28"/><meta property="og:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><meta name="twitter:card" content="summary"/><meta name="twitter:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><link rel="shortcut icon" href="/auspice/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/solarized-dark.min.css"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><script src="/auspice/js/scrollSpy.js"></script><link rel="stylesheet" href="/auspice/css/main.css"/><script src="/auspice/js/codetabs.js"></script></head><body class="sideNavVisible separateOnPageNav"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/auspice/"><img class="logo" src="/auspice/img/logo-light.svg" alt="Auspice"/><h2 class="headerTitleWithLogo">Auspice</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class="siteNavGroupActive"><a href="/auspice/introduction/overview" target="_self">Docs</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><div class="hamburger-menu"><div class="line1"></div><div class="line2"></div><div class="line3"></div></div></div><h2><i>›</i><span>Release Notes</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">Introduction</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/introduction/overview">Overview</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/install">Install Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/how-to-run">How to Run Auspice</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Advanced Functionality</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/second-trees">Displaying multiple trees</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/view-settings">View Settings</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/drag-drop-csv-tsv">Adding extra metadata via CSV/TSV</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/misc">Miscellaneous</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Customising Auspice</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/customise-client/introduction">Customising Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/api">Client Customisation API</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/requests">Requests Made from the Client</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Using a Custom Server</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/server/introduction">Auspice servers</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/api">Server API</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/authentication">Authentication</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Narratives</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/narratives/introduction">Communicating Results Using Narratives</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/how-to-write">Writing a Narrative</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/create-pdf">Converting a narrative to PDF</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Release Notes</h3><ul class=""><li class="navListItem navListItemActive"><a class="navItem" href="/auspice/releases/changelog">Changelog</a></li><li class="navListItem"><a class="navItem" href="/auspice/releases/v2">Auspice Version 2.0</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Contributing</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/contributing/overview">Contributing to Auspice development</a></li></ul></div></div></section></div><script>
+<!DOCTYPE html><html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Changelog · Auspice</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="## version 2.12.0 - 2020/04/08"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Changelog · Auspice"/><meta property="og:type" content="website"/><meta property="og:url" content="https://nextstrain.github.io/auspice/"/><meta property="og:description" content="## version 2.12.0 - 2020/04/08"/><meta property="og:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><meta name="twitter:card" content="summary"/><meta name="twitter:image" content="https://nextstrain.github.io/auspice/img/icon.svg"/><link rel="shortcut icon" href="/auspice/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/solarized-dark.min.css"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><script src="/auspice/js/scrollSpy.js"></script><link rel="stylesheet" href="/auspice/css/main.css"/><script src="/auspice/js/codetabs.js"></script></head><body class="sideNavVisible separateOnPageNav"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/auspice/"><img class="logo" src="/auspice/img/logo-light.svg" alt="Auspice"/><h2 class="headerTitleWithLogo">Auspice</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class="siteNavGroupActive"><a href="/auspice/introduction/overview" target="_self">Docs</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><div class="hamburger-menu"><div class="line1"></div><div class="line2"></div><div class="line3"></div></div></div><h2><i>›</i><span>Release Notes</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">Introduction</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/introduction/overview">Overview</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/install">Install Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/introduction/how-to-run">How to Run Auspice</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Advanced Functionality</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/second-trees">Displaying multiple trees</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/view-settings">View Settings</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/drag-drop-csv-tsv">Adding extra metadata via CSV/TSV</a></li><li class="navListItem"><a class="navItem" href="/auspice/advanced-functionality/misc">Miscellaneous</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Customising Auspice</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/customise-client/introduction">Customising Auspice</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/api">Client Customisation API</a></li><li class="navListItem"><a class="navItem" href="/auspice/customise-client/requests">Requests Made from the Client</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Using a Custom Server</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/server/introduction">Auspice servers</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/api">Server API</a></li><li class="navListItem"><a class="navItem" href="/auspice/server/authentication">Authentication</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Narratives</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/narratives/introduction">Communicating Results Using Narratives</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/how-to-write">Writing a Narrative</a></li><li class="navListItem"><a class="navItem" href="/auspice/narratives/create-pdf">Converting a narrative to PDF</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Release Notes</h3><ul class=""><li class="navListItem navListItemActive"><a class="navItem" href="/auspice/releases/changelog">Changelog</a></li><li class="navListItem"><a class="navItem" href="/auspice/releases/v2">Auspice Version 2.0</a></li></ul></div><div class="navGroup"><h3 class="navGroupCategoryTitle">Contributing</h3><ul class=""><li class="navListItem"><a class="navItem" href="/auspice/contributing/overview">Contributing to Auspice development</a></li></ul></div></div></section></div><script>
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+        </script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Changelog</h1></header><article><div><span><h2><a class="anchor" aria-hidden="true" id="version-2120-2020-04-08"></a><a href="#version-2120-2020-04-08" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.12.0 - 2020/04/08</h2>
+<ul>
+<li>Add a legend to the map! <a href="https://github.com/nextstrain/auspice/pull/935">See PR 935</a></li>
+<li>Improve the animation smoothness, especially for datasets with limited temporal range. <a href="https://github.com/nextstrain/auspice/pull/920">See PR 920</a></li>
+<li>Add Japanese translation <a href="https://github.com/nextstrain/auspice/pull/1045">See PR 1045</a></li>
+<li>Reinstate the <code>lang</code> URL query to allow the URL to choose the language.</li>
+<li>Remove unnecessary lodash code from the bundles. <a href="https://github.com/nextstrain/auspice/pull/1018">See PR 1018</a></li>
+<li>Update how the <code>Root</code> component is imported. <a href="https://github.com/nextstrain/auspice/pull/1029">See PR 1029</a></li>
+<li>Fix errors in the sizing of the map buttons. <a href="https://github.com/nextstrain/auspice/pull/1040">See PR 1040</a></li>
+<li>Improve rendering of tree tip labels by only counting the selected (visible) tips. <a href="https://github.com/nextstrain/auspice/pull/1043">See PR 1043</a></li>
+</ul>
+<h2><a class="anchor" aria-hidden="true" id="version-2114-2020-04-04"></a><a href="#version-2114-2020-04-04" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.11.4 - 2020/04/04</h2>
+<ul>
+<li>Temporarily remove SVG gradients in the tree due to bugs in multiple browsers. <a href="https://github.com/nextstrain/auspice/pull/1042">See PR 1042</a></li>
+</ul>
+<h2><a class="anchor" aria-hidden="true" id="version-2113-2020-04-02"></a><a href="#version-2113-2020-04-02" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.11.3 - 2020/04/02</h2>
+<ul>
+<li>Add Portuguese translation. <a href="https://github.com/nextstrain/auspice/pull/1017">See PR 1017</a></li>
+<li>Fig bug where some branches would not display on certain browsers. <a href="https://github.com/nextstrain/auspice/pull/1022">See PR 1022</a></li>
+<li>Fix bug with selected dates shown when no genomes were selected. <a href="https://github.com/nextstrain/auspice/pull/1011">See PR 1011</a></li>
+<li>Show <code>--includeTiming</code> argument when viewing help (<code>--help</code>).</li>
+<li>Add second node version to TravisCI.  <a href="https://github.com/nextstrain/auspice/pull/1023">See PR 1023</a></li>
+<li>Fix docs typo. <a href="https://github.com/nextstrain/auspice/pull/1027">See PR 1027</a></li>
+</ul>
+<h2><a class="anchor" aria-hidden="true" id="version-2112-2020-03-30"></a><a href="#version-2112-2020-03-30" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.11.2 - 2020/03/30</h2>
+<ul>
+<li>Add French translation - <a href="https://github.com/nextstrain/auspice/pull/1020">See PR 1020</a></li>
+<li>Improve rendering of long strain names in strain search - <a href="https://github.com/nextstrain/auspice/pull/1026">See PR 1026</a></li>
+<li>Lithuanian translation fixes</li>
+</ul>
+<h2><a class="anchor" aria-hidden="true" id="version-2111-2020-03-28"></a><a href="#version-2111-2020-03-28" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 2.11.1 - 2020/03/28</h2>
 <ul>
 <li>Add Lithuanian translation</li>
 <li>Fig bugs in translation strings which contained <code>:</code> or <code>.</code></li>
@@ -960,4 +990,4 @@ <h2><a class="anchor" aria-hidden="true" id="version-171-2017-10-31"></a><a href
 </ul>
 <h2><a class="anchor" aria-hidden="true" id="version-170-2017-10-17"></a><a href="#version-170-2017-10-17" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version 1.7.0 - 2017/10/17</h2>
 <h2><a class="anchor" aria-hidden="true" id="version-2018-01-18"></a><a href="#version-2018-01-18" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>version  - 2018/01/18</h2>
-</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/create-pdf"><span class="arrow-prev">← </span><span>Converting a narrative to PDF</span></a><a class="docs-next button" href="/auspice/releases/v2"><span>Auspice Version 2.0</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#version-2111-2020-03-28">version 2.11.1 - 2020/03/28</a></li><li><a href="#version-2110-2020-03-27">version 2.11.0 - 2020/03/27</a></li><li><a href="#version-2100-2020-03-24">version 2.10.0 - 2020/03/24</a></li><li><a href="#version-291-2020-03-23">version 2.9.1 - 2020/03/23</a></li><li><a href="#version-290-2020-03-23">version 2.9.0 - 2020/03/23</a></li><li><a href="#version-281-2020-03-20">version 2.8.1 - 2020/03/20</a></li><li><a href="#version-280-2020-03-20">version 2.8.0 - 2020/03/20</a></li><li><a href="#version-270-2020-03-15">version 2.7.0 - 2020/03/15</a></li><li><a href="#version-260-2020-03-09">version 2.6.0 - 2020/03/09</a></li><li><a href="#version-257-2020-03-09">version 2.5.7 - 2020/03/09</a></li><li><a href="#version-256-2020-03-09">version 2.5.6 - 2020/03/09</a></li><li><a href="#version-255-2020-03-04">version 2.5.5 - 2020/03/04</a></li><li><a href="#version-254-2020-02-26">version 2.5.4 - 2020/02/26</a></li><li><a href="#version-253-2020-02-12">version 2.5.3 - 2020/02/12</a></li><li><a href="#version-252-2020-02-11">version 2.5.2 - 2020/02/11</a></li><li><a href="#version-251-2020-02-07">version 2.5.1 - 2020/02/07</a></li><li><a href="#version-250-2020-02-05">version 2.5.0 - 2020/02/05</a></li><li><a href="#version-241-2020-02-01">version 2.4.1 - 2020/02/01</a></li><li><a href="#version-240-2020-01-31">version 2.4.0 - 2020/01/31</a></li><li><a href="#version-237-2020-01-30">version 2.3.7 - 2020/01/30</a></li><li><a href="#version-236-2020-01-30">version 2.3.6 - 2020/01/30</a></li><li><a href="#version-235-2020-01-28">version 2.3.5 - 2020/01/28</a></li><li><a href="#version-234-2020-01-28">version 2.3.4 - 2020/01/28</a></li><li><a href="#version-233-2020-01-27">version 2.3.3 - 2020/01/27</a></li><li><a href="#version-232-2020-01-24">version 2.3.2 - 2020/01/24</a></li><li><a href="#version-231-2020-01-24">version 2.3.1 - 2020/01/24</a></li><li><a href="#version-230-2020-01-23">version 2.3.0 - 2020/01/23</a></li><li><a href="#version-224-2020-01-11">version 2.2.4 - 2020/01/11</a></li><li><a href="#version-223-2020-01-06">version 2.2.3 - 2020/01/06</a></li><li><a href="#version-222-2020-01-03">version 2.2.2 - 2020/01/03</a></li><li><a href="#version-221-2020-01-03">version 2.2.1 - 2020/01/03</a></li><li><a href="#version-220-2019-12-16">version 2.2.0 - 2019/12/16</a></li><li><a href="#version-210-2019-11-15">version 2.1.0 - 2019/11/15</a></li><li><a href="#version-203-2019-11-06">version 2.0.3 - 2019/11/06</a></li><li><a href="#version-202-2019-10-30">version 2.0.2 - 2019/10/30</a></li><li><a href="#version-201-2019-10-25">version 2.0.1 - 2019/10/25</a></li><li><a href="#version-200-2019-10-21">version 2.0.0 - 2019/10/21</a></li><li><a href="#version-1391-2019-10-21">version 1.39.1 - 2019/10/21</a></li><li><a href="#version-1390-2019-09-12">version 1.39.0 - 2019/09/12</a></li><li><a href="#version-1382-2019-09-06">version 1.38.2 - 2019/09/06</a></li><li><a href="#version-1381-2019-09-06">version 1.38.1 - 2019/09/06</a></li><li><a href="#version-1380-2019-08-29">version 1.38.0 - 2019/08/29</a></li><li><a href="#version-1375-2019-08-09">version 1.37.5 - 2019/08/09</a></li><li><a href="#version-1374-2019-08-04">version 1.37.4 - 2019/08/04</a></li><li><a href="#version-1373-2019-07-29">version 1.37.3 - 2019/07/29</a></li><li><a href="#version-1372-2019-07-20">version 1.37.2 - 2019/07/20</a></li><li><a href="#version-1371-2019-07-13">version 1.37.1 - 2019/07/13</a></li><li><a href="#version-1370-2019-07-09">version 1.37.0 - 2019/07/09</a></li><li><a href="#version-1366-2019-05-18">version 1.36.6 - 2019/05/18</a></li><li><a href="#version-1365-2019-04-17">version 1.36.5 - 2019/04/17</a></li><li><a href="#version-1364-2019-03-16">version 1.36.4 - 2019/03/16</a></li><li><a href="#version-1363-2019-03-11">version 1.36.3 - 2019/03/11</a></li><li><a href="#version-1362-2019-03-04">version 1.36.2 - 2019/03/04</a></li><li><a href="#version-1361-2019-02-27">version 1.36.1 - 2019/02/27</a></li><li><a href="#version-1360-2019-02-25">version 1.36.0 - 2019/02/25</a></li><li><a href="#version-1355-2019-02-08">version 1.35.5 - 2019/02/08</a></li><li><a href="#version-1354-2019-01-28">version 1.35.4 - 2019/01/28</a></li><li><a href="#version-1353-2019-01-25">version 1.35.3 - 2019/01/25</a></li><li><a href="#version-1352-2019-01-16">version 1.35.2 - 2019/01/16</a></li><li><a href="#version-1344-2019-01-15">version 1.34.4 - 2019/01/15</a></li><li><a href="#version-1343-2018-12-18">version 1.34.3 - 2018/12/18</a></li><li><a href="#version-1342-2018-12-05">version 1.34.2 - 2018/12/05</a></li><li><a href="#version-1341-2018-11-29">version 1.34.1 - 2018/11/29</a></li><li><a href="#version-1340-2018-11-19">version 1.34.0 - 2018/11/19</a></li><li><a href="#version-1330-2018-11-18">version 1.33.0 - 2018/11/18</a></li><li><a href="#version-1320-2018-11-02">version 1.32.0 - 2018/11/02</a></li><li><a href="#version-1310-2018-10-29">version 1.31.0 - 2018/10/29</a></li><li><a href="#version-1303-2018-09-19">version 1.30.3 - 2018/09/19</a></li><li><a href="#version-1302-2018-09-07">version 1.30.2 - 2018/09/07</a></li><li><a href="#version-1301-2018-09-05">version 1.30.1 - 2018/09/05</a></li><li><a href="#version-1300-2018-09-05">version 1.30.0 - 2018/09/05</a></li><li><a href="#version-1290-2018-08-31">version 1.29.0 - 2018/08/31</a><ul class="toc-headings"><li><a href="#narrative-improvements">Narrative improvements</a></li></ul></li><li><a href="#version-1280-2018-08-25">version 1.28.0 - 2018/08/25</a></li><li><a href="#version-1271-2018-08-24">version 1.27.1 - 2018/08/24</a></li><li><a href="#version-1270-2018-08-20">version 1.27.0 - 2018/08/20</a></li><li><a href="#version-1260-2018-08-20">version 1.26.0 - 2018/08/20</a></li><li><a href="#version-1252-2018-08-17">version 1.25.2 - 2018/08/17</a></li><li><a href="#version-1251-2018-08-10">version 1.25.1 - 2018/08/10</a></li><li><a href="#version-1250-2018-08-09">version 1.25.0 - 2018/08/09</a></li><li><a href="#version-1241-2018-08-08">version 1.24.1 - 2018/08/08</a></li><li><a href="#version-1240-2018-08-05">version 1.24.0 - 2018/08/05</a></li><li><a href="#version-1232-2018-07-30">version 1.23.2 - 2018/07/30</a></li><li><a href="#version-1231-2018-07-30">version 1.23.1 - 2018/07/30</a></li><li><a href="#version-1230-2018-07-28">version 1.23.0 - 2018/07/28</a></li><li><a href="#version-1223-2018-07-19">version 1.22.3 - 2018/07/19</a></li><li><a href="#version-1222-2018-07-10">version 1.22.2 - 2018/07/10</a></li><li><a href="#version-1221-2018-07-09">version 1.22.1 - 2018/07/09</a></li><li><a href="#version-1220-2018-07-03">version 1.22.0 - 2018/07/03</a></li><li><a href="#version-1213-2018-06-27">version 1.21.3 - 2018/06/27</a></li><li><a href="#version-1212-2018-06-07">version 1.21.2 - 2018/06/07</a></li><li><a href="#version-1211-2018-06-04">version 1.21.1 - 2018/06/04</a></li><li><a href="#version-1210-2018-06-01">version 1.21.0 - 2018/06/01</a></li><li><a href="#version-1203-2018-05-30">version 1.20.3 - 2018/05/30</a></li><li><a href="#version-1202-2018-05-21">version 1.20.2 - 2018/05/21</a></li><li><a href="#version-1201-2018-05-21">version 1.20.1 - 2018/05/21</a></li><li><a href="#version-1200-2018-05-15">version 1.20.0 - 2018/05/15</a></li><li><a href="#version-1191-2018-05-09">version 1.19.1 - 2018/05/09</a></li><li><a href="#version-1190-2018-05-09">version 1.19.0 - 2018/05/09</a></li><li><a href="#version-11810-2018-05-07">version 1.18.10 - 2018/05/07</a></li><li><a href="#version-1189-2018-05-03">version 1.18.9 - 2018/05/03</a></li><li><a href="#version-1188-2018-05-02">version 1.18.8 - 2018/05/02</a></li><li><a href="#version-1187-2018-05-02">version 1.18.7 - 2018/05/02</a></li><li><a href="#version-1186-2018-04-30">version 1.18.6 - 2018/04/30</a></li><li><a href="#version-1185-2018-04-27">version 1.18.5 - 2018/04/27</a></li><li><a href="#version-1184-2018-04-26">version 1.18.4 - 2018/04/26</a></li><li><a href="#version-1183-2018-04-23">version 1.18.3 - 2018/04/23</a></li><li><a href="#version-1182-2018-04-16">version 1.18.2 - 2018/04/16</a></li><li><a href="#version-1181-2018-04-15">version 1.18.1 - 2018/04/15</a></li><li><a href="#version-1180-2018-04-14">version 1.18.0 - 2018/04/14</a></li><li><a href="#version-1174-2018-04-10">version 1.17.4 - 2018/04/10</a></li><li><a href="#version-1173-2018-04-04">version 1.17.3 - 2018/04/04</a></li><li><a href="#version-1172-2018-04-02">version 1.17.2 - 2018/04/02</a></li><li><a href="#version-1171-2018-03-28">version 1.17.1 - 2018/03/28</a></li><li><a href="#version-1170-2018-03-26">version 1.17.0 - 2018/03/26</a></li><li><a href="#version-1165-2018-03-26">version 1.16.5 - 2018/03/26</a></li><li><a href="#version-1164-2018-03-22">version 1.16.4 - 2018/03/22</a></li><li><a href="#version-1163-2018-03-21">version 1.16.3 - 2018/03/21</a></li><li><a href="#version-1162-2018-03-21">version 1.16.2 - 2018/03/21</a></li><li><a href="#version-1161-2018-03-16">version 1.16.1 - 2018/03/16</a></li><li><a href="#version-1160-2018-03-16">version 1.16.0 - 2018/03/16</a><ul class="toc-headings"><li><a href="#browser-support">Browser support</a></li></ul></li><li><a href="#version-1151-2018-03-14">version 1.15.1 - 2018/03/14</a></li><li><a href="#version-1150-2018-03-12">version 1.15.0 - 2018/03/12</a></li><li><a href="#version-1144-2018-03-05">version 1.14.4 - 2018/03/05</a></li><li><a href="#version-1143-2018-03-01">version 1.14.3 - 2018/03/01</a></li><li><a href="#version-1142-2018-02-28">version 1.14.2 - 2018/02/28</a></li><li><a href="#version-1141-2018-02-27">version 1.14.1 - 2018/02/27</a></li><li><a href="#version-1140-2018-02-27">version 1.14.0 - 2018/02/27</a><ul class="toc-headings"><li><a href="#features">Features</a></li><li><a href="#internals-1">Internals</a></li></ul></li><li><a href="#version-1132-2018-02-26">version 1.13.2 - 2018/02/26</a></li><li><a href="#version-1131-2018-02-26">version 1.13.1 - 2018/02/26</a></li><li><a href="#version-1130-2018-02-26">version 1.13.0 - 2018/02/26</a><ul class="toc-headings"><li><a href="#features-1">Features</a></li><li><a href="#internals-2">Internals</a></li></ul></li><li><a href="#version-1120-2018-02-14">version 1.12.0 - 2018/02/14</a><ul class="toc-headings"><li><a href="#features-2">Features</a></li><li><a href="#internals-3">Internals</a></li></ul></li><li><a href="#version-1110-2018-02-05">version 1.11.0 - 2018/02/05</a><ul class="toc-headings"><li><a href="#features-3">Features</a></li><li><a href="#internals-4">Internals</a></li></ul></li><li><a href="#version-1100-2018-02-05">version 1.10.0 - 2018/02/05</a><ul class="toc-headings"><li><a href="#features-4">Features</a></li><li><a href="#internals-5">Internals</a></li></ul></li><li><a href="#version-190-2018-01-30">version 1.9.0 - 2018/01/30</a><ul class="toc-headings"><li><a href="#animation">Animation</a></li><li><a href="#misc">misc</a></li></ul></li><li><a href="#version-180-2018-01-18">version 1.8.0 - 2018/01/18</a></li><li><a href="#version-172-2018-1-4">version 1.7.2 - 2018/1/4</a></li><li><a href="#version-171-2017-10-31">version 1.7.1 - 2017/10/31</a></li><li><a href="#version-170-2017-10-17">version 1.7.0 - 2017/10/17</a></li><li><a href="#version-2018-01-18">version  - 2018/01/18</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
\ No newline at end of file
+</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/14/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/narratives/create-pdf"><span class="arrow-prev">← </span><span>Converting a narrative to PDF</span></a><a class="docs-next button" href="/auspice/releases/v2"><span>Auspice Version 2.0</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#version-2120-2020-04-08">version 2.12.0 - 2020/04/08</a></li><li><a href="#version-2114-2020-04-04">version 2.11.4 - 2020/04/04</a></li><li><a href="#version-2113-2020-04-02">version 2.11.3 - 2020/04/02</a></li><li><a href="#version-2112-2020-03-30">version 2.11.2 - 2020/03/30</a></li><li><a href="#version-2111-2020-03-28">version 2.11.1 - 2020/03/28</a></li><li><a href="#version-2110-2020-03-27">version 2.11.0 - 2020/03/27</a></li><li><a href="#version-2100-2020-03-24">version 2.10.0 - 2020/03/24</a></li><li><a href="#version-291-2020-03-23">version 2.9.1 - 2020/03/23</a></li><li><a href="#version-290-2020-03-23">version 2.9.0 - 2020/03/23</a></li><li><a href="#version-281-2020-03-20">version 2.8.1 - 2020/03/20</a></li><li><a href="#version-280-2020-03-20">version 2.8.0 - 2020/03/20</a></li><li><a href="#version-270-2020-03-15">version 2.7.0 - 2020/03/15</a></li><li><a href="#version-260-2020-03-09">version 2.6.0 - 2020/03/09</a></li><li><a href="#version-257-2020-03-09">version 2.5.7 - 2020/03/09</a></li><li><a href="#version-256-2020-03-09">version 2.5.6 - 2020/03/09</a></li><li><a href="#version-255-2020-03-04">version 2.5.5 - 2020/03/04</a></li><li><a href="#version-254-2020-02-26">version 2.5.4 - 2020/02/26</a></li><li><a href="#version-253-2020-02-12">version 2.5.3 - 2020/02/12</a></li><li><a href="#version-252-2020-02-11">version 2.5.2 - 2020/02/11</a></li><li><a href="#version-251-2020-02-07">version 2.5.1 - 2020/02/07</a></li><li><a href="#version-250-2020-02-05">version 2.5.0 - 2020/02/05</a></li><li><a href="#version-241-2020-02-01">version 2.4.1 - 2020/02/01</a></li><li><a href="#version-240-2020-01-31">version 2.4.0 - 2020/01/31</a></li><li><a href="#version-237-2020-01-30">version 2.3.7 - 2020/01/30</a></li><li><a href="#version-236-2020-01-30">version 2.3.6 - 2020/01/30</a></li><li><a href="#version-235-2020-01-28">version 2.3.5 - 2020/01/28</a></li><li><a href="#version-234-2020-01-28">version 2.3.4 - 2020/01/28</a></li><li><a href="#version-233-2020-01-27">version 2.3.3 - 2020/01/27</a></li><li><a href="#version-232-2020-01-24">version 2.3.2 - 2020/01/24</a></li><li><a href="#version-231-2020-01-24">version 2.3.1 - 2020/01/24</a></li><li><a href="#version-230-2020-01-23">version 2.3.0 - 2020/01/23</a></li><li><a href="#version-224-2020-01-11">version 2.2.4 - 2020/01/11</a></li><li><a href="#version-223-2020-01-06">version 2.2.3 - 2020/01/06</a></li><li><a href="#version-222-2020-01-03">version 2.2.2 - 2020/01/03</a></li><li><a href="#version-221-2020-01-03">version 2.2.1 - 2020/01/03</a></li><li><a href="#version-220-2019-12-16">version 2.2.0 - 2019/12/16</a></li><li><a href="#version-210-2019-11-15">version 2.1.0 - 2019/11/15</a></li><li><a href="#version-203-2019-11-06">version 2.0.3 - 2019/11/06</a></li><li><a href="#version-202-2019-10-30">version 2.0.2 - 2019/10/30</a></li><li><a href="#version-201-2019-10-25">version 2.0.1 - 2019/10/25</a></li><li><a href="#version-200-2019-10-21">version 2.0.0 - 2019/10/21</a></li><li><a href="#version-1391-2019-10-21">version 1.39.1 - 2019/10/21</a></li><li><a href="#version-1390-2019-09-12">version 1.39.0 - 2019/09/12</a></li><li><a href="#version-1382-2019-09-06">version 1.38.2 - 2019/09/06</a></li><li><a href="#version-1381-2019-09-06">version 1.38.1 - 2019/09/06</a></li><li><a href="#version-1380-2019-08-29">version 1.38.0 - 2019/08/29</a></li><li><a href="#version-1375-2019-08-09">version 1.37.5 - 2019/08/09</a></li><li><a href="#version-1374-2019-08-04">version 1.37.4 - 2019/08/04</a></li><li><a href="#version-1373-2019-07-29">version 1.37.3 - 2019/07/29</a></li><li><a href="#version-1372-2019-07-20">version 1.37.2 - 2019/07/20</a></li><li><a href="#version-1371-2019-07-13">version 1.37.1 - 2019/07/13</a></li><li><a href="#version-1370-2019-07-09">version 1.37.0 - 2019/07/09</a></li><li><a href="#version-1366-2019-05-18">version 1.36.6 - 2019/05/18</a></li><li><a href="#version-1365-2019-04-17">version 1.36.5 - 2019/04/17</a></li><li><a href="#version-1364-2019-03-16">version 1.36.4 - 2019/03/16</a></li><li><a href="#version-1363-2019-03-11">version 1.36.3 - 2019/03/11</a></li><li><a href="#version-1362-2019-03-04">version 1.36.2 - 2019/03/04</a></li><li><a href="#version-1361-2019-02-27">version 1.36.1 - 2019/02/27</a></li><li><a href="#version-1360-2019-02-25">version 1.36.0 - 2019/02/25</a></li><li><a href="#version-1355-2019-02-08">version 1.35.5 - 2019/02/08</a></li><li><a href="#version-1354-2019-01-28">version 1.35.4 - 2019/01/28</a></li><li><a href="#version-1353-2019-01-25">version 1.35.3 - 2019/01/25</a></li><li><a href="#version-1352-2019-01-16">version 1.35.2 - 2019/01/16</a></li><li><a href="#version-1344-2019-01-15">version 1.34.4 - 2019/01/15</a></li><li><a href="#version-1343-2018-12-18">version 1.34.3 - 2018/12/18</a></li><li><a href="#version-1342-2018-12-05">version 1.34.2 - 2018/12/05</a></li><li><a href="#version-1341-2018-11-29">version 1.34.1 - 2018/11/29</a></li><li><a href="#version-1340-2018-11-19">version 1.34.0 - 2018/11/19</a></li><li><a href="#version-1330-2018-11-18">version 1.33.0 - 2018/11/18</a></li><li><a href="#version-1320-2018-11-02">version 1.32.0 - 2018/11/02</a></li><li><a href="#version-1310-2018-10-29">version 1.31.0 - 2018/10/29</a></li><li><a href="#version-1303-2018-09-19">version 1.30.3 - 2018/09/19</a></li><li><a href="#version-1302-2018-09-07">version 1.30.2 - 2018/09/07</a></li><li><a href="#version-1301-2018-09-05">version 1.30.1 - 2018/09/05</a></li><li><a href="#version-1300-2018-09-05">version 1.30.0 - 2018/09/05</a></li><li><a href="#version-1290-2018-08-31">version 1.29.0 - 2018/08/31</a><ul class="toc-headings"><li><a href="#narrative-improvements">Narrative improvements</a></li></ul></li><li><a href="#version-1280-2018-08-25">version 1.28.0 - 2018/08/25</a></li><li><a href="#version-1271-2018-08-24">version 1.27.1 - 2018/08/24</a></li><li><a href="#version-1270-2018-08-20">version 1.27.0 - 2018/08/20</a></li><li><a href="#version-1260-2018-08-20">version 1.26.0 - 2018/08/20</a></li><li><a href="#version-1252-2018-08-17">version 1.25.2 - 2018/08/17</a></li><li><a href="#version-1251-2018-08-10">version 1.25.1 - 2018/08/10</a></li><li><a href="#version-1250-2018-08-09">version 1.25.0 - 2018/08/09</a></li><li><a href="#version-1241-2018-08-08">version 1.24.1 - 2018/08/08</a></li><li><a href="#version-1240-2018-08-05">version 1.24.0 - 2018/08/05</a></li><li><a href="#version-1232-2018-07-30">version 1.23.2 - 2018/07/30</a></li><li><a href="#version-1231-2018-07-30">version 1.23.1 - 2018/07/30</a></li><li><a href="#version-1230-2018-07-28">version 1.23.0 - 2018/07/28</a></li><li><a href="#version-1223-2018-07-19">version 1.22.3 - 2018/07/19</a></li><li><a href="#version-1222-2018-07-10">version 1.22.2 - 2018/07/10</a></li><li><a href="#version-1221-2018-07-09">version 1.22.1 - 2018/07/09</a></li><li><a href="#version-1220-2018-07-03">version 1.22.0 - 2018/07/03</a></li><li><a href="#version-1213-2018-06-27">version 1.21.3 - 2018/06/27</a></li><li><a href="#version-1212-2018-06-07">version 1.21.2 - 2018/06/07</a></li><li><a href="#version-1211-2018-06-04">version 1.21.1 - 2018/06/04</a></li><li><a href="#version-1210-2018-06-01">version 1.21.0 - 2018/06/01</a></li><li><a href="#version-1203-2018-05-30">version 1.20.3 - 2018/05/30</a></li><li><a href="#version-1202-2018-05-21">version 1.20.2 - 2018/05/21</a></li><li><a href="#version-1201-2018-05-21">version 1.20.1 - 2018/05/21</a></li><li><a href="#version-1200-2018-05-15">version 1.20.0 - 2018/05/15</a></li><li><a href="#version-1191-2018-05-09">version 1.19.1 - 2018/05/09</a></li><li><a href="#version-1190-2018-05-09">version 1.19.0 - 2018/05/09</a></li><li><a href="#version-11810-2018-05-07">version 1.18.10 - 2018/05/07</a></li><li><a href="#version-1189-2018-05-03">version 1.18.9 - 2018/05/03</a></li><li><a href="#version-1188-2018-05-02">version 1.18.8 - 2018/05/02</a></li><li><a href="#version-1187-2018-05-02">version 1.18.7 - 2018/05/02</a></li><li><a href="#version-1186-2018-04-30">version 1.18.6 - 2018/04/30</a></li><li><a href="#version-1185-2018-04-27">version 1.18.5 - 2018/04/27</a></li><li><a href="#version-1184-2018-04-26">version 1.18.4 - 2018/04/26</a></li><li><a href="#version-1183-2018-04-23">version 1.18.3 - 2018/04/23</a></li><li><a href="#version-1182-2018-04-16">version 1.18.2 - 2018/04/16</a></li><li><a href="#version-1181-2018-04-15">version 1.18.1 - 2018/04/15</a></li><li><a href="#version-1180-2018-04-14">version 1.18.0 - 2018/04/14</a></li><li><a href="#version-1174-2018-04-10">version 1.17.4 - 2018/04/10</a></li><li><a href="#version-1173-2018-04-04">version 1.17.3 - 2018/04/04</a></li><li><a href="#version-1172-2018-04-02">version 1.17.2 - 2018/04/02</a></li><li><a href="#version-1171-2018-03-28">version 1.17.1 - 2018/03/28</a></li><li><a href="#version-1170-2018-03-26">version 1.17.0 - 2018/03/26</a></li><li><a href="#version-1165-2018-03-26">version 1.16.5 - 2018/03/26</a></li><li><a href="#version-1164-2018-03-22">version 1.16.4 - 2018/03/22</a></li><li><a href="#version-1163-2018-03-21">version 1.16.3 - 2018/03/21</a></li><li><a href="#version-1162-2018-03-21">version 1.16.2 - 2018/03/21</a></li><li><a href="#version-1161-2018-03-16">version 1.16.1 - 2018/03/16</a></li><li><a href="#version-1160-2018-03-16">version 1.16.0 - 2018/03/16</a><ul class="toc-headings"><li><a href="#browser-support">Browser support</a></li></ul></li><li><a href="#version-1151-2018-03-14">version 1.15.1 - 2018/03/14</a></li><li><a href="#version-1150-2018-03-12">version 1.15.0 - 2018/03/12</a></li><li><a href="#version-1144-2018-03-05">version 1.14.4 - 2018/03/05</a></li><li><a href="#version-1143-2018-03-01">version 1.14.3 - 2018/03/01</a></li><li><a href="#version-1142-2018-02-28">version 1.14.2 - 2018/02/28</a></li><li><a href="#version-1141-2018-02-27">version 1.14.1 - 2018/02/27</a></li><li><a href="#version-1140-2018-02-27">version 1.14.0 - 2018/02/27</a><ul class="toc-headings"><li><a href="#features">Features</a></li><li><a href="#internals-1">Internals</a></li></ul></li><li><a href="#version-1132-2018-02-26">version 1.13.2 - 2018/02/26</a></li><li><a href="#version-1131-2018-02-26">version 1.13.1 - 2018/02/26</a></li><li><a href="#version-1130-2018-02-26">version 1.13.0 - 2018/02/26</a><ul class="toc-headings"><li><a href="#features-1">Features</a></li><li><a href="#internals-2">Internals</a></li></ul></li><li><a href="#version-1120-2018-02-14">version 1.12.0 - 2018/02/14</a><ul class="toc-headings"><li><a href="#features-2">Features</a></li><li><a href="#internals-3">Internals</a></li></ul></li><li><a href="#version-1110-2018-02-05">version 1.11.0 - 2018/02/05</a><ul class="toc-headings"><li><a href="#features-3">Features</a></li><li><a href="#internals-4">Internals</a></li></ul></li><li><a href="#version-1100-2018-02-05">version 1.10.0 - 2018/02/05</a><ul class="toc-headings"><li><a href="#features-4">Features</a></li><li><a href="#internals-5">Internals</a></li></ul></li><li><a href="#version-190-2018-01-30">version 1.9.0 - 2018/01/30</a><ul class="toc-headings"><li><a href="#animation">Animation</a></li><li><a href="#misc">misc</a></li></ul></li><li><a href="#version-180-2018-01-18">version 1.8.0 - 2018/01/18</a></li><li><a href="#version-172-2018-1-4">version 1.7.2 - 2018/1/4</a></li><li><a href="#version-171-2017-10-31">version 1.7.1 - 2017/10/31</a></li><li><a href="#version-170-2017-10-17">version 1.7.0 - 2017/10/17</a></li><li><a href="#version-2018-01-18">version  - 2018/01/18</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
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diff --git a/docs/server/introduction.html b/docs/server/introduction.html
index f05662c47..715af507e 100644
--- a/docs/server/introduction.html
+++ b/docs/server/introduction.html
@@ -78,7 +78,7 @@ <h2><a class="anchor" aria-hidden="true" id="get-requests"></a><a href="#get-req
 Similarly, nextstrain.org is a server which has handlers for these three API endpoints, so if you visit <a href="https://nextstrain.org/charon/getAvailable">nextstrain.org/charon/getAvailable</a> you'll see Nextstrain's available datasets.</p>
 <p>See <a href="/auspice/server/api">the server API</a> for details about each of these requests.</p>
 <blockquote>
-<p>Note that &quot;/charon&quot; can be changed to any address you wich by customising the client at build time.
+<p>Note that &quot;/charon&quot; can be changed to any address you wish by customising the client at build time.
 See <a href="../customise-client/api">the client-cusomisation API</a> for more details.</p>
 </blockquote>
 <h2><a class="anchor" aria-hidden="true" id="the-default-auspice-server"></a><a href="#the-default-auspice-server" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>The &quot;Default&quot; Auspice Server</h2>
@@ -105,4 +105,4 @@ <h2><a class="anchor" aria-hidden="true" id="deploying-via-heroku"></a><a href="
 <li>Make sure the datasets to be served are either (a) included in your git repo or (b) downloaded by the heroku build pipeline.
 <a href="https://github.com/nextstrain/auspice/blob/master/package.json">We use option (b)</a> by specifing a npm script called <code>heroku-postbuild</code>.</li>
 </ol>
-</span></div></article></div><div class="docLastUpdate"><em>Last updated on 1/2/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/requests"><span class="arrow-prev">← </span><span>Requests Made from the Client</span></a><a class="docs-next button" href="/auspice/server/api"><span>Server API</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#get-requests">GET Requests</a></li><li><a href="#the-quot-default-quot-auspice-server">The &quot;Default&quot; Auspice Server</a></li><li><a href="#customising-the-default-auspice-server">Customising the Default Auspice Server</a></li><li><a href="#writing-your-own-custom-server">Writing Your Own Custom Server</a></li><li><a href="#deploying-via-heroku">Deploying via Heroku</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
\ No newline at end of file
+</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/31/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/requests"><span class="arrow-prev">← </span><span>Requests Made from the Client</span></a><a class="docs-next button" href="/auspice/server/api"><span>Server API</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#get-requests">GET Requests</a></li><li><a href="#the-quot-default-quot-auspice-server">The &quot;Default&quot; Auspice Server</a></li><li><a href="#customising-the-default-auspice-server">Customising the Default Auspice Server</a></li><li><a href="#writing-your-own-custom-server">Writing Your Own Custom Server</a></li><li><a href="#deploying-via-heroku">Deploying via Heroku</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
\ No newline at end of file
diff --git a/docs/server/introduction/index.html b/docs/server/introduction/index.html
index f05662c47..715af507e 100644
--- a/docs/server/introduction/index.html
+++ b/docs/server/introduction/index.html
@@ -78,7 +78,7 @@ <h2><a class="anchor" aria-hidden="true" id="get-requests"></a><a href="#get-req
 Similarly, nextstrain.org is a server which has handlers for these three API endpoints, so if you visit <a href="https://nextstrain.org/charon/getAvailable">nextstrain.org/charon/getAvailable</a> you'll see Nextstrain's available datasets.</p>
 <p>See <a href="/auspice/server/api">the server API</a> for details about each of these requests.</p>
 <blockquote>
-<p>Note that &quot;/charon&quot; can be changed to any address you wich by customising the client at build time.
+<p>Note that &quot;/charon&quot; can be changed to any address you wish by customising the client at build time.
 See <a href="../customise-client/api">the client-cusomisation API</a> for more details.</p>
 </blockquote>
 <h2><a class="anchor" aria-hidden="true" id="the-default-auspice-server"></a><a href="#the-default-auspice-server" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>The &quot;Default&quot; Auspice Server</h2>
@@ -105,4 +105,4 @@ <h2><a class="anchor" aria-hidden="true" id="deploying-via-heroku"></a><a href="
 <li>Make sure the datasets to be served are either (a) included in your git repo or (b) downloaded by the heroku build pipeline.
 <a href="https://github.com/nextstrain/auspice/blob/master/package.json">We use option (b)</a> by specifing a npm script called <code>heroku-postbuild</code>.</li>
 </ol>
-</span></div></article></div><div class="docLastUpdate"><em>Last updated on 1/2/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/requests"><span class="arrow-prev">← </span><span>Requests Made from the Client</span></a><a class="docs-next button" href="/auspice/server/api"><span>Server API</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#get-requests">GET Requests</a></li><li><a href="#the-quot-default-quot-auspice-server">The &quot;Default&quot; Auspice Server</a></li><li><a href="#customising-the-default-auspice-server">Customising the Default Auspice Server</a></li><li><a href="#writing-your-own-custom-server">Writing Your Own Custom Server</a></li><li><a href="#deploying-via-heroku">Deploying via Heroku</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
\ No newline at end of file
+</span></div></article></div><div class="docLastUpdate"><em>Last updated on 3/31/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/customise-client/requests"><span class="arrow-prev">← </span><span>Requests Made from the Client</span></a><a class="docs-next button" href="/auspice/server/api"><span>Server API</span><span class="arrow-next"> →</span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#get-requests">GET Requests</a></li><li><a href="#the-quot-default-quot-auspice-server">The &quot;Default&quot; Auspice Server</a></li><li><a href="#customising-the-default-auspice-server">Customising the Default Auspice Server</a></li><li><a href="#writing-your-own-custom-server">Writing Your Own Custom Server</a></li><li><a href="#deploying-via-heroku">Deploying via Heroku</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
\ No newline at end of file

From 82fb6ce3dbbafbd7afb52661aff8396f7ae2bad3 Mon Sep 17 00:00:00 2001
From: Sidney Bell <sidneymbell@users.noreply.github.com>
Date: Mon, 13 Apr 2020 17:58:47 -0700
Subject: [PATCH 30/30] Tidy up the narratives front matter

---
 cli/server/parseNarrative.js      | 14 +++++++-------
 src/components/narrative/index.js |  3 +--
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/cli/server/parseNarrative.js b/cli/server/parseNarrative.js
index ce1ec262f..9c1940c3d 100644
--- a/cli/server/parseNarrative.js
+++ b/cli/server/parseNarrative.js
@@ -28,14 +28,14 @@ const makeFrontMatterBlock = (frontMatter) => {
   }
   /* create markdown to represent the title page */
   const markdown = [];
-  markdown.push(`# ${frontMatter.title}`);
+  markdown.push(`## ${frontMatter.title}`);
   if (frontMatter.authors) {
     const authors = parseContributors(frontMatter, "authors", "authorLinks");
     if (authors) {
       markdown.push(`### Author: ${authors}`);
       if (frontMatter.affiliations && typeof frontMatter.affiliations === "string") {
         markdown[markdown.length-1] += " <sup> 1 </sup>";
-        markdown.push(`<sup> 1 </sup> ${frontMatter.affiliations}`);
+        markdown.push(`<sub><sup> 1 </sup> ${frontMatter.affiliations}</sub>`);
       }
     }
   }
@@ -45,14 +45,14 @@ const makeFrontMatterBlock = (frontMatter) => {
       markdown.push(`### Translators: ${translators}`);
     }
   }
+  if (frontMatter.abstract && typeof frontMatter.abstract === "string") {
+    markdown.push(`### ${frontMatter.abstract}`);
+  }
   if (frontMatter.date && typeof frontMatter.date === "string") {
-    markdown.push(`### Created: ${frontMatter.date}`);
+    markdown.push(`#### Created: ${frontMatter.date}`);
   }
   if (frontMatter.updated && typeof frontMatter.updated === "string") {
-    markdown.push(`### Updated: ${frontMatter.updated}`);
-  }
-  if (frontMatter.abstract && typeof frontMatter.abstract === "string") {
-    markdown.push(`#### ${frontMatter.abstract}`);
+    markdown.push(`#### Updated: ${frontMatter.updated}`);
   }
 
   const block = new Proxy({}, blockProxyHandler);
diff --git a/src/components/narrative/index.js b/src/components/narrative/index.js
index 25f6906f3..e9cbc45ba 100644
--- a/src/components/narrative/index.js
+++ b/src/components/narrative/index.js
@@ -22,8 +22,7 @@ const progressHeight = 25;
 
 const explanationParagraph=`
   <p class="explanation">
-  Explore the content by scrolling the left hand side (or click on the arrows), and the data visualizations will change accordingly.
-  Clicking "explore the data yourself" (top right of page) will replace this narrative with a set of controls so that you may interact with the data.
+  Explore the narrative by scrolling on the left panel, or click "explore the data yourself" in the top right to interact with the data.
   </p>
 `;