2.12 Expansion and contraction of gene families
According to the orthologs obtained by gene family clustering and the
phylogenetic tree constructed based on single-copy orthologous genes,
the gene families that expanded or contracted in 14 species were
analyzed using CAFÉ (De Bie et al. 2006). A random birth and
death model was used to predict gene family variations along each
lineage of the phylogenetic tree. The P -values were used to
determine the significance of each gene family by comparing conditional
likelihoods derived from a probabilistic graphical model. Significantly
expanded gene families (P values < 0.05) were
performed using a GO term enrichment analysis with EnrichPipeline32
(Beissbarth & Speed 2004; Huang da et al. 2009).