Tree Sequence Exploratory Data Analysis. Currently builds on code base in tsbrowse and retains some of the functionality. tseda adds functionality to view the spatial distribution of population data and connect that information to the genetic structure of the populations.
The input trees file must be tszipped and preprocessed into a
tsbrowse file. Given a trees file data.trees the following
commands perform compression and preprocessing of the file
tszip data.trees
python -m tseda preprocess data.trees.tsz
to produce the output data.trees.tseda. To launch the web app run
python -m tseda serve data.trees.tseda
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| Screenshot of the prototype GNN viewer |
tseda is currently in development. To install the latest dev version from github, run
python -m pip install git+https://github.com/tforest/tseda
- sample set editor to customize sample set definitions, names and colors
- summary statistics (Fst, genealogical nearest neighbours (GNN)) compared and averaged over sample sets
- genealogical nearest neighbour (GNN) analyses of samples
- plots of common summary statistics over sequence length (diversity, Tajimas_D, divergence, Fst)
- marginal tree plots
- pairwise coalescence plots
The package comes with test data files corresponding to an
uncompressed trees file (test.trees), a tszipped trees file
(test.trees.tsz), and two tseda files (test.trees.tseda and
time-calibrated test.trees.tsdate.tseda) residing in tests/data.
To try out the web app, load the file tests/data/test.trees.tseda as
described above.