Index of /arthropods/orthologs/DAPHNIA17/daph10_omcl

 Name                                 Last modified       Size  Description

 Parent Directory                     11-Dec-2017 13:37      -  
 EvigeneOrthoMCLMethods.txt           29-Nov-2017 15:22     2k  
 all_orthomcl.out.gz                  14-Nov-2017 13:48   1.1M  
 daph10omcla-or1inpar-count.tab       14-Nov-2017 13:51     1k  
 daph10omcla-orsinpar-count.tab       14-Nov-2017 13:51     1k  
 daph10omcla-orthomcl-1to1n.tab       14-Nov-2017 13:51    47k  
 daph10omcla-orthomcl-count.tab       14-Nov-2017 13:50   921k  
 daph10omcla-orthomcl-gclass.tab      14-Nov-2017 13:50     1k  
 daph10omcla-orthomcl-gcommon.tab     14-Nov-2017 13:50     1k  
 daph10omcla.aa.qual                  13-Nov-2017 11:31  19.8M  
 daph10omcla.bpo.gz                   14-Nov-2017 08:37   341M  
 daph10omcla.gg.gz                    14-Nov-2017 08:23   775k  
 daph10omcla_dapmaevg14.orpar.tab     14-Nov-2017 14:18  14.8M  
 daph10omcla_dpx17evg.orpar.tab       14-Nov-2017 14:15  16.7M  
 daph10omcla_genes.ugp.txt.gz         15-Nov-2017 15:25   5.5M  
 daph10omcla_genes.ugp.xml            15-Nov-2017 15:48  49.1M  
 daph10omcla_genes.ugp_brief.txt      15-Nov-2017 15:25   6.4M  
 daph10omcla_omclgn.consensus_def.txt 15-Nov-2017 15:25   2.3M  
 daph10omcla_omclgn.tab               14-Nov-2017 13:48   6.4M  
 daph10omcla_omclgn2sum.tab           14-Nov-2017 13:50  14.9M  
 daph10omcla_omclgns2.tab.gz          14-Nov-2017 13:50  41.6M  
 daph10omcla_omsubgrp1.list           14-Nov-2017 13:51   382k  
 daph10omcla_omsubgrp1.names          15-Nov-2017 15:26   254k  
 orthomcl.log                         14-Nov-2017 09:00   113k  
 parameter.log                        14-Nov-2017 09:00     2k  
 run_evgomcl.sh                       08-Nov-2017 21:50     2k  
 run_evgomcltab_old.sh                14-Nov-2017 13:46     1k  
 run_evgomcltabn.sh                   15-Nov-2017 14:19     3k  
 run_evgomclxmln.sh                   15-Nov-2017 15:47     3k  

Evigene Methods for Orthology Assessment
for daph10_omcl gene clustering of Daphnia, Insects and Fishes (+human)

Method Steps: 
1.  collect species gene proteins, primary isoform only, for 10 species, in daph10omcl.aa
    each header has species tag:ID prefix.  Extract gene Names from aa headers for use below.
2.  blastp -db daph10omcl.aa -query daph10omcl.aa -evalue 1e-5 -outfmt 7 -out daph10omcl.aa.blastp
3.  tabulate daph10omcl.aa.blastp and run OrthoMCL (Evigene repackage), using MCL Markov clustering
    run_evgomcl.sh script
4.  outputs: daph10omcla.bpo,.gg are intermediate inputs to orthomcl_evg.pl, 
    all_orthomcl.out and tmp/ files are cluster outputs.
5.  tabulate orthomcl.out to summary tables and annotated gene groups, with input gene.names (from aa headers)
    run_evgomcltabn.sh script
6.  summary and gene group outputs:
    intermediate tables are daph10omcla_omclgn.tab (OMCL group per gene), 
      daph10omcla_omclgns2.tab (pairwise genes per omcl group), 
      daph10omcla_omclgn2sum.tab shorter of daph10omcla_omclgns2.
    daph10omcla-orthomcl-count.tab table of species presence/gene count per group
    daph10omcla-orthomcl-gclass.tab, gcommon.tab : brief summaries per species of group types (orlog,parlog,..)
    daph10omcla-orthomcl-1to1n.tab, table of 1:1 ortholog species presence (from count.tab)
    daph10omcla-orsinpar-count.tab and or1inpar-count tab, species matrix of ortholog counts shared by species pairs,
	orsinpar = all orthologs, or1inpar = closest ortholog (orlog1) only.  Matrix diagonal is paralog count
        per species
    daph10omcla_dpx17evg.orpar.tab, daph10omcla_dapmaevg14.orpar.tab : per species table of ortholog, paralog
       pairings, from daph10omcla_omclgns2.tab that has all species
    daph10omcla_genes.ugp.txt, daph10omcla_genes.ugp.xml : annotated gene groups, with consensus group name,
       counts, and per-species genes listed
    daph10omcla_genes.ugp_brief.txt : from ugp.txt, stripping long list of species genes (one line/group)