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@lczech lczech released this May 17, 2020 · 21 commits to master since this release

Notable Changes

  • Change writer classes to use new output targets functionality
  • Add Fastq handling: reading, writing, iterating
  • Add phred quality score handling
  • Add gzip output support and gzip streams
  • Add date/time conversion functions

Further Changes

  • Add a lot of refinements to existing functionality
  • Improve support and fix issues for build platforms and compilers
  • Refine error messages for file handling
  • Several speedups, improvements, and bug fixes
Assets 2

@lczech lczech released this Feb 6, 2020 · 237 commits to master since this release

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

  • Add a lot of more tutorials for all parts of genesis.
  • Reduce memory footprint of Squash Clustering.
  • Add Robinson-Foulds (RF) distance functions.
  • Several bugfixes and refinements.
Assets 2

@lczech lczech released this May 14, 2019 · 291 commits to master since this release

Notable Changes

  • Refine input stream reading.
  • Refine phylip reading.
Assets 2

@lczech lczech released this May 10, 2019 · 295 commits to master since this release

Notable Changes

  • Add support for old versions 1 and 2 of the jplace standard.
  • Add minimal tree function for easier tree experimentation.
  • Fix some issues occurring on Mac and with other compilers.
  • Fix issues found by clang sanitizer and similar tools.
  • Fix some bugs, refine some code, speed up some functions.
Assets 2

@lczech lczech released this Mar 13, 2019 · 336 commits to master since this release

This is a long overdue release that adds a lot of new features, and refactors existing ones. It breaks compatibility with previous releases.

Important Changes

  • Refactor design and usage of input reading functions/classes.
  • Rename DefaultTree to CommonTree.
  • Use dereferencing iterator for Tree members.
  • Refactor several smaller classes and functions for usability.

Notable Changes

  • Add transparent gzib and zlib support for input reading.
  • Add adaptation of Phylogenetic Isometric Log-Ratio (PhILR) Transform to phylogenetic placements.
  • Add Placement-Factorization, an adaptation of Phylofactorization to phylogenetic placements.
  • Add Generalized Linear Models (GLM).
  • Add Multi-Dimensional Scaling (MDS).
  • Add Taxonomy to Tree functions.
  • Add Tree/Sample rerooting and subtree deletion functions.
  • Add Subtree class, add iterator support for subtrees.

Further Changes

  • Add heat tree / heat map visualization.
  • Add several statistics functions.
  • Add a lot (!) of smaller auxiliary functions and features.
  • Fix several bugs, implement several speedups and improvements.
Assets 2

@lczech lczech released this Oct 10, 2018 · 571 commits to master since this release

Notable Changes

  • Add Sequence abundances.
  • Rename and change several Tree functions and classes.
  • Refine hashing functions and classes.
  • Add several Taxonomy functions.
  • Add and change k-means functions.
  • Add Matrix Writer class.
  • Many bugfixes and refinements.
Assets 2

@lczech lczech released this Mar 20, 2018 · 659 commits to master since this release

Notable Changes

  • Refactor Node Histogram Distance.
  • Refactor bipartition functions.
  • Add more Color and Svg functions.
  • Add and improved Tree drawing functions.
  • Add Matrix iterators.
  • Add DataFrame and MruCache classes.
  • Add hash and sequence signature functions.
  • Add many convenience and helper functions.
  • Refactor some functions and classes.
  • Speedups in many functions.
  • Some bugfixes.
Assets 2

@lczech lczech released this Dec 10, 2017 · 817 commits to master since this release

Notable Changes

  • Fix regex issue with gcc5.
  • Fix numercial issue in geodesy test case.
  • Fix missing header include.
Assets 2

@lczech lczech released this Dec 10, 2017 · 821 commits to master since this release

Notable Changes

  • Add Color Palette class and more Color features and lists.
  • Simplify consensus sequence calculations, add Cavener's method.
  • Add some geodesy functions.
  • Add Matrix Reader class.
  • Speedups in Jplace Reader and Node Distance Matrix.
Assets 2

@lczech lczech released this Nov 16, 2017 · 850 commits to master since this release

Notable Changes

  • Add per-module headers.
  • Better CMake support for using Genesis as a library.
  • Refactor Node Histogram Distance to also use negative axis.
  • Add some helper functions and speedups.
  • Change default out of range behaviour of Histogram.
Assets 2
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