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- 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
- 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
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.
- 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.
- Add support for old versions 1 and 2 of the
- 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.
This is a long overdue release that adds a lot of new features, and refactors existing ones. It breaks compatibility with previous releases.
- 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.
- 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.
- 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.
- 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.
- Refactor Node Histogram Distance.
- Refactor bipartition functions.
- Add more Color and Svg functions.
- Add and improved Tree drawing functions.
- Add Matrix iterators.
- Add hash and sequence signature functions.
- Add many convenience and helper functions.
- Refactor some functions and classes.
- Speedups in many functions.
- Some bugfixes.
- 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.
- 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.