Gappa Versions Save

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.