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Mar 27, 2023
- updated to now save morpholog tables · ccba7188
  Niko Papadopoulos authored 1 year ago
  
  v1.2
  
  ccba7188
Jan 25, 2023
- now running MMseqs2 with -s 7 · 32da861d
  Niko Papadopoulos authored 2 years ago
  
  v1.1
  
  32da861d
- revisit MorF-EggNOG overlap (Table 3) · 30b67fc7
  Niko Papadopoulos authored 2 years ago
  
  30b67fc7
Jan 24, 2023
- looked at EC of second-best morphologs and why they sometimes disagree; looked... · c29d13de
  Niko Papadopoulos authored 2 years ago
  
  looked at EC of second-best morphologs and why they sometimes disagree; looked at available choanos for HGT candidates
  c29d13de
Jan 12, 2023
- freshened up README · 9ea3b8ae
  Niko Papadopoulos authored 2 years ago
  
  9ea3b8ae
- finally removing Untitled.ipynb · 7450654c
  Niko Papadopoulos authored 2 years ago
  
  7450654c
- removed image · cef41e2a
  Niko Papadopoulos authored 2 years ago
  
  cef41e2a
- added HMMER annotation performance · 7c3fa17d
  Niko Papadopoulos authored 2 years ago
  
  7c3fa17d
Jan 09, 2023
- added HMMER analysis, morpholog phylogenetic distribution, and additional info on table3 · 7f88d077
  Niko Papadopoulos authored 2 years ago
  
  7f88d077
Dec 28, 2022
- rerun to produce figures · e71eca47
  Niko Papadopoulos authored 2 years ago
  
  e71eca47
Dec 21, 2022
- fixed EC calculation for remote species; answered top N morpholog question. · 78a6b710
  Niko Papadopoulos authored 2 years ago
  
  78a6b710
Dec 20, 2022
- comparison of top N hits at certain score margin done; discovered bug with EC comparison · 3047dac4
  Niko Papadopoulos authored 2 years ago
  
  3047dac4
- Merge branch 'main' of git.embl.de:grp-arendt/CoFFE · 9409104d
  Niko Papadopoulos authored 2 years ago
  
  9409104d
- how well is protein function captured by the top morphologs? · d9c064b8
  Niko Papadopoulos authored 2 years ago
  
  d9c064b8
- update GO analysis with GO depth · ed65d494
  Fabian Ruperti authored 2 years ago
  
  ed65d494
Dec 16, 2022
- Merge branch 'main' of git.embl.de:grp-arendt/CoFFE · 05713f7d
  Fabian Ruperti authored 2 years ago
  
  05713f7d
- GO term comparison notebook finished · 62ebdb07
  Fabian Ruperti authored 2 years ago
  
  62ebdb07
- renaming revision notebooks; added yeast/arabidopsis-human comparison · bc9cc294
  Niko Papadopoulos authored 2 years ago
  
  bc9cc294
Dec 15, 2022
- revision GO term comparison · 97404076
  Fabian Ruperti authored 2 years ago
  
  97404076
- added statistical comparison of avg pLDDT distributions · 2c08e415
  Niko Papadopoulos authored 2 years ago
  
  2c08e415
Sep 01, 2022
- added model species foldseek searches · bbda981a
  nikolaos.papadopoulos@embl.de authored 2 years ago
  
  bbda981a
Aug 17, 2022
- Merge branch 'main' of git.embl.de:grp-arendt/CoFFE into main · 711581d3
  Nikolaos Papadopoulos authored 2 years ago
  
  711581d3
- fixed ModelArchive bugs (protein names/models, protein query length); added... · 9d321e6a
  Nikolaos Papadopoulos authored 2 years ago
  
  fixed ModelArchive bugs (protein names/models, protein query length); added AFDB self comparison as per editors' request
  9d321e6a
Aug 02, 2022
- reworking analysis to accommodate new UniProt RESTful API · e0fada09
  Nikolaos Papadopoulos authored 2 years ago
  
  e0fada09
- updated README with aims, license · 59641e28
  Niko Papadopoulos authored 2 years ago
  
  v1.0
  
  59641e28
- update scripts to new paths, new conda env name · 9e154601
  Niko Papadopoulos authored 2 years ago
  
  9e154601
- Add LICENSE · ee0e19cf
  Niko Papadopoulos authored 2 years ago
  
  ee0e19cf
Aug 01, 2022
- now manual workaround for PDB ID mapping · 5276fe26
  Nikolaos Papadopoulos authored 2 years ago
  
  5276fe26
Jul 29, 2022
- temp saving of AFDB, SWP parquets now possible; minor file structure changes · 8dd17e2e
  Nikolaos Papadopoulos authored 2 years ago
  
  8dd17e2e
Jul 28, 2022
- Merge branch 'main' of git.embl.de:grp-arendt/CoFFE into main · 6a5ed0e3
  Nikolaos Papadopoulos authored 2 years ago
  
  6a5ed0e3
- migrating read/write to scripts and out of notebook · f14f1db2
  Nikolaos Papadopoulos authored 2 years ago
  
  f14f1db2
- Add scripts to reproduce the sequence and profile search based analysis · 62a76855
  Milot Mirdita authored 2 years ago
  
  62a76855
Jul 15, 2022
- Merge branch 'npapadop-main-patch-23276' into 'main' · abf52890
  Niko Papadopoulos authored 2 years ago
  
  updated README to reflect the stage of the project See merge request grp-arendt/CoFFE!2
  abf52890
- updated README to reflect the stage of the project · fb68c6cc
  Niko Papadopoulos authored 2 years ago
  
  fb68c6cc
Jul 13, 2022
- cleanup and preparation for submission · e619cd50
  Nikolaos Papadopoulos authored 2 years ago
  
  e619cd50
Jul 12, 2022
- staging for submission · 1c4a5e31
  Nikolaos Papadopoulos authored 2 years ago
  
  1c4a5e31
Jul 07, 2022
- merged conflicts in DEG revisited · d4323513
  Nikolaos Papadopoulos authored 2 years ago
  
  d4323513
- rerunning scripts for plots · b261f98e
  Nikolaos Papadopoulos authored 2 years ago
  
  b261f98e
Jul 06, 2022
- update annotation_categories for suppl fig 2.1, 2.2 and 2.3 · bb34d6e7
  Fabian Ruperti authored 2 years ago
  
  bb34d6e7
- updated suppl-annotaion-categories to make suppl fig 2.1 and 2.2 · 76394efc
  Fabian Ruperti authored 2 years ago
  
  76394efc