Commits · 79fbf64a729780352e01f6d3e86beeb4b3200b6a · remy / OrthoFinder

Nov 12, 2019
- Merge branch 'master' of https://gitlab.mbb.univ-montp2.fr/remy/orthofinder · 79fbf64a
  remy authored 5 years ago
  
  79fbf64a
- more explicit error message · ccb7a5f2
  remy authored 5 years ago
  
  ccb7a5f2
- check ipsecies · c2e2a5fd
  remy authored 5 years ago
  
  c2e2a5fd
- tempfile was not correctly flushed and closed · 4e0858b7
  remy authored 5 years ago
  
  4e0858b7
- renaming a function · 2bfe9705
  remy authored 5 years ago
  
  2bfe9705
Nov 11, 2019
- tempfile was nt created at the right place · 544a328b
  remy authored 5 years ago
  
  544a328b
- still some bugs but nevertheless it gives some results · 06675bb2
  remy authored 5 years ago
  
  06675bb2
- bugs fixed · 5862116d
  remy authored 5 years ago
  
  5862116d
- Normalize is not compatible with other options. It is a one shot operation · a681390d
  remy authored 5 years ago
  
  a681390d
Nov 10, 2019
- adding method to add a new csv file based on normalized scores · 17f9044b
  remy authored 5 years ago
  
  17f9044b
Nov 08, 2019
- missing parenthesis · eb517248
  remy authored 5 years ago
  
  eb517248
- adding necessary addtionnal conditions for Normalize option · bc24ca34
  remy authored 5 years ago
  
  bc24ca34
- Normalize option · 389d0934
  remy authored 5 years ago
  
  389d0934
- adding a DoNormalize function · 02f4a6ba
  remy authored 5 years ago
  
  02f4a6ba
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