Commits · a6e7f5a04ebba86cf0ff8d7fe49d14e5715801d8 · remy / OrthoFinder

Nov 07, 2019
- adding a normalize option · a6e7f5a0
  remy authored 5 years ago
  
  a6e7f5a0
Nov 06, 2019
- Support python 2.7 & 3+, resolves #270 · d9dd44c9
  David Emms authored 5 years ago
  
  d9dd44c9
- Towards support for python 3 · 9cc74166
  David Emms authored 5 years ago
  
  9cc74166
Nov 04, 2019
- Don't keep blank lines in input fasta files, resolves #275 · b2b39d34
  David Emms authored 5 years ago
  
  b2b39d34
- Check for good accessions at start of run, resolves #298 · 5737d1a5
  David Emms authored 5 years ago
  
  5737d1a5
- Allow for failing MSA, resolves #298 · f1c69e79
  David Emms authored 5 years ago
  
  f1c69e79
Oct 22, 2019
- Only open ortholog files once to avoid sophos slowdown · 87d3c77f
  David Emms authored 5 years ago
  
  View commits for tag 2.3.7 2.3.7
  
  87d3c77f
Oct 18, 2019
- Error if species tree not available · 680818ef
  David Emms authored 5 years ago
  
  680818ef
- Only need to print path to top-level results · 36761651
  David Emms authored 5 years ago
  
  36761651
- Add citations file · c7979101
  David Emms authored 5 years ago
  
  c7979101
- Skip missing trees in STAG, resolves #293 · a2b7bd14
  David Emms authored 5 years ago
  
  a2b7bd14
Oct 17, 2019
- typo · 695b4916
  David Emms authored 5 years ago
  
  695b4916
Oct 11, 2019
- primary_transcripts.py file for users to process input files · e17cf0a1
  David Emms authored 5 years ago
  
  e17cf0a1
- Remove non-core binaries · 322bf0b4
  David Emms authored 5 years ago
  
  322bf0b4
- Setup to download and run with no installation · 3fe0e5c6
  David Emms authored 5 years ago
  
  3fe0e5c6
Oct 04, 2019
- When checking input files don't reject if sequences are lowercase, resolves #285 · 3edb4bf1
  David Emms authored 5 years ago
  
  3edb4bf1
- Fix writing of misplaced genes to file, resolves #288 · 33a12a28
  David Emms authored 5 years ago
  
  33a12a28
Aug 20, 2019
- Add iqtree and trim option, currently requires edited noisy · 0f80bacc
  David Emms authored 5 years ago
  
  0f80bacc
Aug 16, 2019
- Run trees2ologs standalone · 9e7dbc9c
  David Emms authored 5 years ago
  
  9e7dbc9c
Aug 07, 2019
- Root unresolved gene trees and write support values if available · 2d6dcffe
  David Emms authored 5 years ago
  
  2d6dcffe
Jul 18, 2019
- Identify species-specific orthogroups · 220e3ba4
  David Emms authored 5 years ago
  
  220e3ba4
- Close multiprocessing pools to reduce RAM usage · 06f10ff4
  David Emms authored 5 years ago
  
  06f10ff4
Jul 02, 2019
- Fully parallise tree inference in default mode · 07cae23a
  David Emms authored 5 years ago
  
  07cae23a
Jun 10, 2019
- Update mmseqs command · e76e4dd1
  David Emms authored 5 years ago
  
  e76e4dd1
- Ignore MMseqs suffixes for long sequences, resolves #269 · 52c17702
  David Emms authored 5 years ago
  
  52c17702
- Merge branch 'master' of https://github.com/davidemms/OrthoFinder · 2576dbb6
  David Emms authored 5 years ago
  
  2576dbb6
Jun 05, 2019
- Update README.md · 40f07acc
  David Emms authored 5 years ago
  
  40f07acc
Jun 03, 2019
- Update README.md · 80cf4bfc
  David Emms authored 5 years ago
  
  80cf4bfc
May 29, 2019
- Spell check README file · db208f47
  David Emms authored 5 years ago
  
  db208f47
- Update README.md · 4fa2a00e
  David Emms authored 5 years ago
  
  4fa2a00e
- Update README.md · d2a28c93
  David Emms authored 5 years ago
  
  d2a28c93
- Formatting README · dcc3f023
  David Emms authored 5 years ago
  
  dcc3f023
- Expand README section on the results files · 809cc330
  David Emms authored 5 years ago
  
  809cc330
- Add details for more of the results files to README · 2073f0bd
  David Emms authored 5 years ago
  
  2073f0bd
- Minor text changes to README.md · fc102855
  David Emms authored 5 years ago
  
  fc102855
May 01, 2019
- Include required binaries in release package · 3ce2ce78
  David Emms authored 6 years ago
  
  3ce2ce78
Apr 29, 2019
- Avoid hang that can occur using pipe with subprocess, resolves #145 · e360ba89
  David Emms authored 6 years ago
  
  View commits for tag 2.3.3 2.3.3
  
  e360ba89
Apr 25, 2019
- Add options to test gene tree resolution outside of OrthoFinder · 5947fee3
  David Emms authored 6 years ago
  
  5947fee3
Apr 08, 2019
- Allow root age to be specified for make_ultrametric tool · 0076b054
  David Emms authored 6 years ago
  
  0076b054
Mar 21, 2019
- Add script to convert trees to ultrametric · 1ea99cec
  David Emms authored 6 years ago
  
  1ea99cec