2.6.0

Summary of Changes from 2.5.0 to 2.6.0

New features:

• produce orthoxml files according to v0.5 of orthoxml
  (https://github.com/qfo/orthoxml/releases/tag/v0.5)

• Map-SeqNum-ID.txt contains an additional column indicating
  which proteins were selected as main isoforms.

Bug Fixes:

• exclude all but main isoform variant from the HierarchicalGroups.orthoxml
  output (#8)

• fixes an issue with parsing splicing information for genomes with
  many splicing variants.

• minor improvements in the documentation.

v2.5.0

Summary of Changes from 2.4.2 to 2.5.0

New features:

• introduces new variable AuxDataPath in parameters file that allows to
  specify the path where auxillary datafiles are stored.

• provide docker container on dockerhub for OMA standalone.
  dessimozlab/oma_standalone

Bug Fixes:

• fixes problems running OMA standalone on debian buster clusters (gh-issue #3)

• minor improvements in the documentation.

V2.4.0

Merge branch 'develop'

* develop: (33 commits)
  minor update of release notes
  fixes problem with gethogs_bottom_up if passing a species tree
  sync default and toyexample parameter file
  minor extensions and fixes on the manual
  update release noteswq
  bit of additional docu on SkipVerification
  perf impr: check nr neighbors right away
  improving bottom-up hog integration
  cleanup unused stuff from profiling, keep idea to limit Graph size
  lot's of additional profiling stuff.
  create virtualenv with python3 or python2 for hog_bottom_up
  update darwin repo path
  update manual with new OutgroupSpecies parameter
  update parameter file for ToyExample
  adding OutgroupSpecies parameter
  fixes typos and whitespaces
  change HOG inference to bottom-up by default
  Adding checks in OMA.drw and disabling removal of raw output when ckpt present
  fixed typo
  include precise volume info of OmaStandalone paper
  ...