genesis v0.18.0

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.

genesis v0.17.0

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.

genesis v0.16.0

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.

genesis v0.15.0

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.

genesis v0.14.0

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.

genesis v0.13.0

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.

genesis v0.12.1

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.

genesis v0.12.0

Notable Changes

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

genesis v0.11.1

Notable Changes

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

genesis v0.11.0

Notable Changes

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