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[Arthropod] Recent arthropod orthology data sets (Re: Daphnia has the most ancestral genes)

Don Gilbert via arthropod%40net.bio.net (by gilbertd from bio.indiana.edu)
Tue Feb 2 13:37:44 EST 2010

For those of you who want to look at recent Arthropod orthology analyses,
here is a list I have, probably not complete, but a few of these include
Daphnia and Ixodes and more recent insects, to balance the Dipteran
perspective of arthropod genes.  Of these, I think the phylomedb.org 
Acyrthosiphon set is perhaps the most valuable, even lacking Ixodes.  
Toni Gabaldon provides his alignment and tree data sets, so one can do post 
analyses such as measuring which species have more ancestral genes.

-- Don

  Acyrthosiphon pisum phylome
  Toni Gabaldon and colleagues using phylogenetic orthology 
  include 14 recent arthropod genomes up to daphnia,
  aphid, nasonia, but not ixodes, along with human, worm, ciona outgroups
  review of methods: http://genomebiology.com/2008/9/10/235

  Evgeny Zdobnov and colleagues,
  recent gene sets for arthropods, includes Daphnia and Ixodes,
  and recent insects Aphid, Pediculus, Nasonia.

  current release has 2008/2009 data, with 1,200 completely sequenced genomes,
  includes daphnia, recent insects, but not ixodes

phigs.org, ca 2006-2007 arthropod and eukaryote genomes
  using phylogenetic orthology methods, Jeff Boore and JGI
  colleagues, now offline, but I've a subset including Daphnia,
  several insects, and vertebrates (no ixodes)

  OrthoMCL-DB, current release from 2009 has 138 genomes across the tree,
  however arthropods include only insect genomes

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