A toolkit for analyzing and visualizing phylogenetic (placement) data
GPL-3.0 License
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Published by lczech over 1 year ago
Published by lczech almost 2 years ago
Published by lczech about 2 years ago
filter
commandPublished by lczech almost 3 years ago
clean-tree
commandPublished by lczech almost 3 years ago
filter
commandmerge
commandlwr-distribution
command and helper scriptlwr
command into lwr-histogram
and lwr-list
--distant-label
option for assign
commandrandom
to simulate
Published by lczech over 3 years ago
Version bump to fix the version number. It was somehow stuck at v0.6.1
Published by lczech over 3 years ago
Published by lczech about 4 years ago
gappa examine assign
commandPublished 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 almost 5 years ago
Published by lczech about 5 years ago
This is mostly a maintenance and quality-of-life update that improves usability and cleans up the interface.
Published by lczech over 5 years ago
jplace
standard versions 1 and 2.prepare random-placements
command.Published by lczech over 5 years ago
Unfortunately, this release has a broken commit hash for the genesis version. It hence does not work when using CMake
to download the genesis dependency. Instead, you have to use git clone --recursive
or some other git
command to pull the correct genesis version. You have to pull this commit.
We do not fix this release, so please download a more recent release instead if needed. Sorry for the inconvenience.
analyze placement-factorization
command.edit multiplicity
command.edit split
command.prepare random-alignment
command.prepare random-tree
command.prepare taxonomy-tree
command.Published by lczech over 5 years ago
Changes:
assign
command (#5).Published by lczech almost 6 years ago
Initial release that starts version counting. For now, the tool should not be considered stable. Anything may change at any time. More commands and features will be added. This release is mainly intended as a point of reference (see #4).