v0.4.3

Ignore missing or ambiguous sites

• All scripts now have the option to ignore missing or ambiguous bases when
  running an analysis with HyDe. Just add --ignore_amb_sites as a flag
  at the command line.

v0.4.2

• Fixing issue with plotting.
• Also adding ability to read lower case base pairs and ambiguity codes (a, g, t, c, n, r,...).

v0.4.0

Removing dependence on hyde_cpp

• The hyde_cpp executable has been deprecated in favor of using the
  *_hyde.py scripts, which are just as fast. It will be available
  as its own GitHub repository for legacy purposes: link.

• The phyde.analyze submodule has been removed, and all functions calling the
  hyde_cpp program have been either modified or removed.

• We anticipate that this will make the installation process simpler, and will
  allow us to distribute the software as purely a Python package (w/ Cython for speed).

v0.3.3

New multithreaded scripts

• All of the *_hyde.py scripts now have multithreaded versions:
  run_hyde_mp.py, individual_hyde_mp.py, and bootstrap_hyde_mp.py.
  Parallelization with these scripts works best with data sets that have a lot of species.
  We use the multiprocess module, which will need to be installed: pip install multiprocess.

• We also added a quiet option (-q or --quiet) to suppress printing to stdout
  while the program is running.

v0.3.1

v0.3.1

Bug fixes from major updates in v0.3.0:

• Corrected bootstrap_hyde.py output.
• Bootstrap class now correctly calculates # of bootstrap reps.
• Better handling of files with extra empty line at the end.

v0.3.0

Changes introducing incompatibilities with previous versions:

• The ability to do bootstrapping was removed from hyde_cpp. This
  functionality is now provided by the bootstrap_hyde.py script. All
  scripts relying on bootstrapping with hyde_cpp have been changed
  accordingly.

New workflow scripts:

We introduce a new workflow for HyDe using three main Python scripts that can be
called from the command line. They are automatically installed with the phyde
module. A new input file is also introduced for specifying specific triples that
are to be tested using the methods implemented in the scripts (see below).

• run_hyde.py: this script remains largely the same as in previous versions.
  We have added the ability to test specific hypotheses rather than running a
  full analysis (all triples in all directions) as well.
• individual_hyde.py: this new script takes a table of specified triples
  and tests all individuals in the hybrid population separately.
• bootstrap_hyde.py: this new script will bootstrap resample individuals
  within the hybrid populations that are specified by the table of triples.

Input format for specifying triples:

The three scripts listed above can take as input a three column table where each
row specifies the names of taxa that are to be tested for hybridization.
The order is (Parent 1, Hybrid, Parent 2) as below:

sp1 sp2 sp3
sp1 sp2 sp4
sp2 sp3 sp4
.
.
.

The individual_hyde.py and bootstrap_hyde.py files can also take output files
from previous runs of HyDe. These contain header information that the scripts will
automatically check for and will then parse the first three columns of the file.

v0.2.3

Final release of v0.2.* series

This release can be used as a legacy version for the old workflow for HyDe (versions 0.1 and 0.2). Ideally users should switch to the newest version.

Patches to existing v0.2.0 release. New build/install procedure for Cython module.

v0.2.0

First release of HyDe.

Features:

• hyde_cpp executable for performing full scale hybridization detection analyses on phylogenomic data sets.

• phyde Python module for performing individual hypothesis tests, parsing and analyzing results from hyde_cpp, plotting, and calculating D-Statistics.