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Created with Raphaël 2.2.027Mar25Jan2412928Dec212016151Sep17Aug2129Jul2815131276129Jun2817151330May2523201918171613129522Apr191312114125Mar22161514updated to now save morpholog tablesv1.2 mainv1.2 mainnow running MMseqs2 with -s 7v1.1v1.1revisit MorF-EggNOG overlap (Table 3)looked at EC of second-best morphologs and why they sometimes disagree; looked at available choanos for HGT candidatesfreshened up READMEfinally removing Untitled.ipynbremoved imageadded HMMER annotation performanceadded HMMER analysis, morpholog phylogenetic distribution, and additional info on table3rerun to produce figuresfixed EC calculation for remote species; answered top N morpholog question.comparison of top N hits at certain score margin done; discovered bug with EC comparisonMerge branch 'main' of git.embl.de:grp-arendt/CoFFEhow well is protein function captured by the top morphologs?update GO analysis with GO depthMerge branch 'main' of git.embl.de:grp-arendt/CoFFEGO term comparison notebook finishedrenaming revision notebooks; added yeast/arabidopsis-human comparisonrevision GO term comparisonadded statistical comparison of avg pLDDT distributionsadded model species foldseek searchesMerge branch 'main' of git.embl.de:grp-arendt/CoFFE into mainfixed ModelArchive bugs (protein names/models, protein query length); added AFDB self comparison as per editors' requestreworking analysis to accommodate new UniProt RESTful APIupdated README with aims, licensev1.0v1.0update scripts to new paths, new conda env nameAdd LICENSEnow manual workaround for PDB ID mappingtemp saving of AFDB, SWP parquets now possible; minor file structure changesMerge branch 'main' of git.embl.de:grp-arendt/CoFFE into mainmigrating read/write to scripts and out of notebookAdd scripts to reproduce the sequence and profile search based analysisMerge branch 'npapadop-main-patch-23276' into 'main'updated README to reflect the stage of the projectcleanup and preparation for submissionstaging for submissionmerged conflicts in DEG revisitedrerunning scripts for plotsupdate annotation_categories for suppl fig 2.1, 2.2 and 2.3updated suppl-annotaion-categories to make suppl fig 2.1 and 2.2