genesis v0.19.0

@lczech lczech released this Mar 20, 2018 · 65 commits to master since this release

Notable Changes

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

genesis v0.18.1

@lczech lczech released this Dec 10, 2017 · 223 commits to master since this release

Notable Changes

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

genesis v0.18.0

@lczech lczech released this Dec 10, 2017 · 227 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.

genesis v0.17.0

@lczech lczech released this Nov 16, 2017 · 256 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.

genesis v0.16.0

@lczech lczech released this Aug 3, 2017 · 289 commits to master since this release

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

@lczech lczech released this Jun 14, 2017 · 352 commits to master since this release

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

@lczech lczech released this Apr 17, 2017 · 368 commits to master since this release

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

@lczech lczech released this Mar 20, 2017 · 422 commits to master since this release

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

@lczech lczech released this Oct 7, 2016 · 699 commits to master since this release

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

@lczech lczech released this Oct 6, 2016 · 704 commits to master since this release

Notable Changes

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