Gene tree/species tree reconcilation

(Held 3/7/2007)

Given a set of putatively orthologous gene families, build gene trees for these and infer speciation/duplication history.

• Rod Page's GeneTree
  • Cotton JA, Page RD.  Going nuclear: gene family evolution and vertebrate phylogeny reconciled.  Proc Biol Sci. 2002 Aug 7;269(1500):1555-61.

• Zmasek and Eddy
  • Zmasek CM, Eddy SR.  A simple algorithm to infer gene duplication and speciation events on a gene tree.  Bioinformatics. 2001 Sep;17(9):821-8.
  • Zmasek CM, Eddy SR.  RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.  BMC Bioinformatics. 2002 May 16;3:14.

• Lars Arvestad
  • Arvestad L, Berglund AC, Lagergren J, Sennblad B.  Bayesian gene/species tree reconciliation and orthology analysis using MCMC.  Bioinformatics. 2003;19 Suppl 1:i7-15.
  • PrIMETV and reconcile

• Supertree construction
  • CLANN - Creevey CJ, McInerney JO.  Clann: investigating phylogenetic information through supertree analyses.  Bioinformatics. 2005 Feb 1;21(3):390-2. Epub 2004 Sep 16.

• See also Phyloinformatics hackathon documentation on gene tree/species tree reconcilation
  • Mike Sanderson's gtp, an implementation of Zmasek and Eddy RIO scores
  • Parsimony approach SoftParsMap

• CAFE
  • Theory and application yeast data Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N.  Estimating the tempo and mode of gene family evolution from comparative genomic data.  Genome Res. 2005 Aug;15(8):1153-60.
  • Application De Bie T, Cristianini N, Demuth JP, Hahn MW.  CAFE: a computational tool for the study of gene family evolution.  Bioinformatics. 2006 May 15;22(10):1269-71. Epub 2006 Mar 16.
  • Application to mammalian data Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW.  The evolution of mammalian gene families.  PLoS ONE. 2006 Dec 20;1:e85.

-- IanHolmes - 07 Mar 2007