genesis

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.

Notable Changes

• Better CMake support for using Genesis as a library.
• Add Squash Clustering.
• Add statistics functions (correlation coefficients, ranking, etc).
• Improvements in Earth Mover's Distance and EdgePCA calculations.
• Improvements in Tree drawing and Matrix functions.
• Various bugfixes and speedups.

Notable Changes

• Add better multiple Newick trees reading support.
• Speedup and refinements in Node Histogram Distance and EdgePCA calculation.
• Add color palettes.
• Add Genesis version name.

Notable Changes

• Add Placement Histograms demo.
• Add K-means clustering, including K-means++ and empty cluster treatment.
• Add Attribute Tree, which supports string maps for Nodes and Edges.
• Add simple k-mer counting functions.
• Improved EMD and EdgePCA calculations: Faster and more flexible.
• Tutorials for Basic Tree usage and for Sequences.

This is an overdue release that contains some major incompatibilities with previous versions.

Important Changes

• Move all library files to lib/genesis subdirectory, to avoid include conflicts.
• All binaries are now all compiled into the bin directory and its subdirectories.

Notable Changes

• Add functions to add Nodes to a Tree.
• Add Tree reroot and ladderize function.
• Add labelled tree function and demo.
• Add EdgePCA function, PCA function and Matrix statistics functions.
• Add Bitmap, better Svg and better Json support.
• Add functions for Taxonomies and Sequences, like pruning by entropy and consensus sequences.
• Refine some functions to work with Sequences, as well as Phylip and Fasta files.
• Refactor Tree reading and writing. More extensible now, more options available.
• Refactor the interface of Sample.
• Major speedups in Earth Movers Distance implementation.

Further Changes

• Add global option for allowing to overwrite files.
• All readers now use the new scanners. The old lexer class is gone.
• Add unity build by default for speedup and better optimization.
• Better support of Pthreads and OpenMP.
• Preparations for reactivation of Python bindings with Pybind11.
• Automatic download of GTest and Pybind11, if needed.
• Add some documentation for existing code.

Notable Changes

• Fix in Tree scaling for "Compare Jplace Files" demo.
• Add scale_all_branch_lengths() function for Sample.
• Allow small tolerance in sum of LWRs for validating a Sample.

Notable Changes

• Add color gradient information to the "Visualize Placement" demo.
• Add circular tree drawing functions.
• Some small fixes and improvements.

Notable Changes

• Fix bug in "Compare Jplace Files" demo program.
• Add some minor functions.

Notable Changes

• Add SHA1 calculation, e.g., for Sequence relabelling.
• Add Expected Distance between Placement Locations (EDPL) functions.

Notable Changes

• Add "Compare Jplace Files" demo.

This release contains some major incompatibilities with previous versions.

Notable Changes

• Refactor Tree template class into normal class. Thus, data on Nodes and Edges is now dynamic instead of static.
• Add functions and classes to work with Sequences, e.g., consensus sequences, filtering, sanitizing.
• Add functionality and algorithms for working with Taxonomies, e.g., iterators, pruning by entropy, arbitrary data on Taxa.
• Add helper classes and functions that will be important later: SVG, RMQ, TwobitVector and more.
• Stall Python support. It's too much work to maintain the bindings while working on the library. Will continue once the API is stable.
• Bugfixes and better C++14 compatibility, plus many internal changes for speedup and improved maintainability.

Notable Changes

• Add many Taxonomy functions.
• Add Taxonomy Reader for CSV files with Taxscriptors.
• Add functions for Trees and distances.
• Add some more functions for Sequences and fasta files.
• Some function renaming for more consistency.
• Update extract clade placement demo to use CSV file instead of clade directory.
• Many bugfixes.

Notable Changes

• Add Taxonomy class and functions.
• Add CsvReader class.
• Move Reader and Writer classes from io to formats.
• Turn Log Warnings into exceptions where reasonable.
• Reading formats works with all new line chars now (including Mac and Win).
• Fix issue with C++14 compiler and make_unique implementation.

Notable Changes

• Finish first working version of the Placement Simulator.
• Speedup for writing Jplace files.
• Fix some issues with g++ and Boost Python.

Notable Changes

• Bugfix in Visualize Placement demo.

Notable Changes

• Add example to "Extract Clade Placements" demo.
• Rename Tree distance functions; add some of their missing implementations.

Notable Changes

• Add normalizing step to "Extract Clade Placements" demo.
• Add Tree::convert_from() function for trees with different template parameters.
• Add new, more flexible EMD implementation, that also takes multiplicities into account.
• Make Sample::add_pquery() function work with Pqueries from different Samples.
• Add some safety measures, documentation etc for some classes.
• Fix some minor bugs.

This release contains a major refactoring of the API. One big step towards a clean, consistent
interface.

The API is still not finished yet. There might be breaking changes in the future.

Notable Changes

• Major API cleanup and changes towards consistency.
  • Major refactoring of many class interfaces.
  • Outsource many class functions to free functions.
  • Move all code into distinct module namespaces.
• Update Python bindings.
• Add manual with first tutorials and demos.
• Make build process ready for release.
• Add continuous integration.

(Re-)Release that changes the license from GNU GPL v2 to v3.

This is not an API-breaking change, but a license-breaking one. As GPL v2 and v3 are incompatible, we increase the version number to make that change visible.

This is a minor release that prepares a change of the license.

Notable Changes

• Restructure the doc directory.
• Restructure the tools directory.
• Move file functions to namespace genesis::utils.