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OrthoFinder v2.3.12 (stable)
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@davidemms davidemms released this 07 May 16:21
· 136 commits to master since this release
2.3.12
94c1148

This is a stable release that fixes any known issues in the previous release.

Which package to download:

  • On Linux download OrthoFinder.tar.gz. This bundles all the required external dependencies (mcl, diamond, fastme) and python libraries and so should run immediately, without any installation being required.
  • On Mac the bioconda package is probably the easiest method: See Bioconda getting started and, once bioconda is set up, run conda install orthofinder
  • On either platform you can run the source code version but you will need to have python and the numpy & scipy libraries installed.
  • On Windows the best way is to install the Windows Subsystem for Linux and then use the linux version
    More detailed instructions here: https://davidemms.github.io/orthofinder_tutorials/alternative-ways-of-getting-OrthoFinder.html

Issues resolved

  • Update primary_transcript.py for python3, resolves #345
  • Vectorise alignment trimming, 45mins->1.5s on 6 species x 3 million base alignment
  • Updates to Manual & README
  • Set OPENBLAS_NUM_THREADS=1, resolves #356
  • Fix reporting of external program error messages
  • Exception.message deprecated in python3, resolves #375
  • Correct handling of species tree without support values, resolves #379
  • Improve handling of commented out species
  • Check at start if open file limit is too low and inform user, resolves #384
Assets 4