1. 12 Nov, 2018 1 commit
  2. 05 Oct, 2018 1 commit
  3. 01 Oct, 2018 1 commit
    • Jorge Navarro Muñoz's avatar
      Input sanitation and update to included MIBiG BGCs · 48579954
      Jorge Navarro Muñoz authored
      - Gene and protein names will have colons in their names substituted by
      underscores to avoid issues further on (colons are used internally to
      split information contained in the sequences' header)
      - Added a new bundle of MIBiG BGCs (version 1.4). Version 1.3 is still
      kept for reproducibility
      48579954
  4. 07 Sep, 2018 1 commit
  5. 03 Sep, 2018 1 commit
  6. 06 Aug, 2018 4 commits
  7. 03 Aug, 2018 3 commits
  8. 19 Jun, 2018 1 commit
  9. 05 Jun, 2018 1 commit
  10. 23 May, 2018 3 commits
  11. 22 May, 2018 1 commit
    • Jorge Navarro Muñoz's avatar
      New feature: domain whitelist · ddf670d0
      Jorge Navarro Muñoz authored
      - Include only BGCs that contain a user-defined list of domain accessions. In
      this case, the list is contained in the domain_whitelist.txt file (which
      already includes an example). Toggle with --domain_whitelist
      ddf670d0
  12. 18 May, 2018 2 commits
  13. 04 May, 2018 4 commits
  14. 03 May, 2018 1 commit
  15. 01 May, 2018 4 commits
  16. 30 Apr, 2018 6 commits
  17. 26 Apr, 2018 1 commit
  18. 13 Apr, 2018 2 commits
  19. 09 Apr, 2018 2 commits
    • Jorge Navarro Muñoz's avatar
      CHANGES IN DEFAULT PARAMETERS · 15c0ce69
      Jorge Navarro Muñoz authored
      - hybrids mode is now default. Use --hybrids-off to turn it off
      - cutoffs now has a single default value: 0.3
      - clans clustering is now activated by default. Use --clans-off to turn
      it off
      - clan_cutoff is now 0.3 0.7 (i.e. will use GCFs defined at 0.3 and will
      form GCC using average distance between GCFs of 0.7 or less)
      15c0ce69
    • Jorge Navarro Muñoz's avatar
      MIBiG mode bugfix · a59c1eb9
      Jorge Navarro Muñoz authored
      Fixes issue #5. Some BGCs in MIBiG that don't have any domains were not
      being removed from the mibig_set
      a59c1eb9