A library for working with phylogenetic and population genetic data.
GPL-3.0 License
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Published by lczech 4 months ago
This is mainly a release to fix the window averaging approach for FST, which was statistically nonsensical in the last release by accident.
Published by lczech 5 months ago
This release is a major clean-up of the population classes and functions. In particular: (1) "Iterator" classes have been renamed to the more appropriate "Stream", and (2) the Variant filtering approach has been completely redesigned to use tags instead of fully removing positions from the stream, allowing us to properly compute per-window averages of statistics.
Published by lczech about 1 year ago
Published by lczech over 1 year ago
Published by lczech almost 2 years ago
Published by lczech about 2 years ago
Published by lczech over 2 years ago
Published by lczech almost 3 years ago
version.hpp
file did not get updated properly with genesis v0.26.0 due to the new year, but also:Published by lczech almost 3 years ago
Population:
Tree:
Utils:
Published by lczech over 3 years ago
This is a long overdue release that adds a lot of new features, and in particular introduces support for population genetics data, methods, and file formats, and adds an (optional) dependency on htslib.
Published by lczech over 4 years ago
Published by lczech over 4 years ago
This is the release that accompanies the publication of our application note
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.
Lucas Czech, Pierre Barbera, and Alexandros Stamatakis.
Bioinformatics, 2020. https://doi.org/10.1093/bioinformatics/btaa070
which is now the official reference to cite when using genesis and gappa.
Published by lczech over 5 years ago
Published by lczech over 5 years ago
jplace
standard.Published by lczech over 5 years ago
This is a long overdue release that adds a lot of new features, and refactors existing ones. It breaks compatibility with previous releases.
Published by lczech about 6 years ago
Published by lczech over 6 years ago
DataFrame
and MruCache
classes.Published by lczech almost 7 years ago
Published by lczech almost 7 years ago