gappa

Notable Changes

• Add GLM coefficient output to Placement-Factorization
• Add Kendall's tau to Edge Correlation
• Fix issue in Assign command

Notable Changes

• Fix bug in Edge PCA transformation table, and add more helpful tables and trees
• Refine CMake OpenMP static linking setup

Notable Changes

• Add per-sample MSA file output in unchunkify, based on the chunked (hashed) query MSA
• Improve SVG output by setting proper document boundaries
• Extend tree output options, in particular for Newick
• Stability fixes for OpenMP and build setup for MacOS
• Fix EDPL histogram empty max value edge case #21

Notable Changes

• Add pendant length filters to filter command

Notable Changes

• Add clean-tree command
• Add taxon name cleaning option to taxonomy tree command
• Fix Newick reader error when reading multiple numeric values of a node

Notable Changes

• Add filter command
• Add merge command
• Add lwr-distribution command and helper script
• Refactor lwr command into lwr-histogram and lwr-list
• Add --distant-label option for assign command
• Rename module random to simulate
• Refine a lot of documentation and option descriptions
• Refine automatic thread number guessing to use OpenMP
• Fix nan issue in KR distance computation

Version bump to fix the version number. It was somehow stuck at v0.6.1

Notable Changes

• Refactor file output to offer suffixes and gz compression
• Fix table input separator char option
• Fix file input gz filtering
• Fix KR distance normalization

Notable Changes

• Add support for multi gz file input
• Add more options to gappa examine assign command
• Refine documentation
• Fix several issues and bugs
• Extend travis test cases

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.

Notable Changes

• Reduce memory footprint of Squash Clustering.

This is mostly a maintenance and quality-of-life update that improves usability and cleans up the interface.

Notable Changes

• Restructure analyze and examine modules.
• Move random data generation commands to own module.
• Add log file option.
• Improve error reporting and logging.
• Add tool commands, citation, license and version.
• Add proper formatting to help messages.
• Refine and add documentation of several commands.
• Several bug fixes.

Notable Changes

• Support for jplace standard versions 1 and 2.
• Add prepare random-placements command.
• Better support for Mac OS.
• Fix https://github.com/bioconda/bioconda-recipes/pull/14765

IMPORTANT

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.

Notable Changes

• Add analyze placement-factorization command.
• Add edit multiplicity command.
• Add edit split command.
• Add prepare random-alignment command.
• Add prepare random-tree command.
• Add prepare taxonomy-tree command.

Changes:

• Add and change the output options for assign command (#5).
• Fix #6, where some large files were not parsed correctly.

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).