OrthoMCL clustering of proteins among arthropod genomes

Daphnia Ortholog Groups Search, DAPHNIA17 water flea genes, 2017 Fish Ortholog Groups Search, FISH12 of Killifish genome project, 2014 Arthropod Ortholog Groups Search, EvidentialGene ARP7, 2014 Search Arthropod gene clusters ARP1: (2008.08)   ...   ARP2: (2009.12) for:   >Limit to genes in these taxa Mosquitoes any None 1 1+ 2+ 1 or 0 Fruitflies any None 1 1+ 2+ 1 or 0 Hymenoptera any None 1 1+ 2+ 1 or 0 Other insects any None 1 1+ 2+ 1 or 0 Other Ar'pods any None 1 1+ 2+ 1 or 0 >Limit to genes in these species Aedes any None 1 1+ 2+ 1 or 0 Anopheles any None 1 1+ 2+ 1 or 0 Culex any None 1 1+ 2+ 1 or 0 DrosMel any None 1 1+ 2+ 1 or 0 DrosMoj any None 1 1+ 2+ 1 or 0 DrosPse any None 1 1+ 2+ 1 or 0 Apis any None 1 1+ 2+ 1 or 0 Nasonia any None 1 1+ 2+ 1 or 0 Bombyx any None 1 1+ 2+ 1 or 0 Tribolium any None 1 1+ 2+ 1 or 0 Aphid any None 1 1+ 2+ 1 or 0 Pediculus any None 1 1+ 2+ 1 or 0 Daphnia any None 1 1+ 2+ 1 or 0 Ixodes any None 1 1+ 2+ 1 or 0 See this Summary of Arthropod ortholog clusters

Phylogenetic trees: Fitch:phenogram or Neighor:tree >Newick tree of Arthropods # Arthropod gene group phylogeny (v. ARP2, 2010.01, D. Gilbert) # from OrthoMCL/BlastP analysis of 14 species proteomes, # distance matrix of best recip orthologs (using formula D2 of # doi:10.1093/nar/gki181), followed by Phylip Fitch distance trees, # J=250, rooted at Ixodes ((((((( ((DrosMel:0.16946,DrosPse:0.27553):0.03808,DrosMoj:0.29297):0.37569, ((Culex:0.28236,Aedes:0.20645):0.14114,Anopheles:0.27578):0.19011):0.10815, Bombyx:0.57957):0.01218,Tribolium:0.46032):0.02573, (Apis:0.32155,Nasonia:0.56158):0.17971):0.01871, Pediculus:0.41209):0.02903,Aphid:0.81649):0.10212, Daphnia:0.75698,Ixodes:0.72260);

 Name                     Last modified       Size  Description

 Parent Directory         23-Apr-2019 14:05      -  
 ARP1/                    24-Jul-2011 23:13      -  
 ARP2/                    24-Jul-2011 23:06      -  
 ARP3x/                   25-Feb-2012 13:12      -  
 ARP7/                    24-Nov-2014 18:16      -  
 DAPHNIA17/               11-Dec-2017 13:37      -  
 FISH12/                  11-Dec-2017 13:35      -  
 arthropod-arp2-pheno.pdf 04-Jan-2010 17:01     2k  
 arthropod-arp2-pheno.png 04-Jan-2010 17:07    44k  
 arthropod-arp2-tree.pdf  04-Jan-2010 17:02     1k  
 arthropod-arp2-tree.png  04-Jan-2010 17:06    84k  
 genetrees/               26-Jul-2011 22:21      -  

Citations:
  D. Gilbert, OrthoMCL clustering among 14 arthropod proteomes (ARP2).
  http://arthropods.eugenes.org/arthropods/
  Dec. 2009, gilbertd@indiana.edu

  D. Gilbert, OrthoMCL clustering among 13 arthropod proteomes (ARP1).
  http://insects.eugenes.org/arthropods/
  Aug. 2008, gilbertd@indiana.edu

  OrthoMCL: http://www.orthomcl.org/
   Li Li, Christian J. Stoeckert, Jr., and David S. Roos
   OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res. 2003 13: 2178-2189.
   Feng Chen, Aaron J. Mackey, Jeroen K. Vermunt, and David S. Roos
   Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes. PLoS ONE 2007 2(
4): e383.