2.5 ∣ Identification of contracted and expanded gene families
Gene families were constructed through a hierarchical clustering
algorithm and ‘all against all’ BLASTP. The alignments with high-scoring
segment pairs (HSPs) were conjoined for each gene pair by solar. To
identify homologous gene-pairs, more than 30% coverage of the aligned
regions in both homologous genes was required. We determined the
expansion and contraction of orthologous gene families by comparing the
cluster size differences between the ancestor and other species using
the CAFÉ (Version 1.6) program. A random death model was used to study
changes of gene families along each lineage of phylogenetic tree. A
probabilistic graphical model (PGM) was introduced to the probability of
transitions in gene family size from parent to child nod phylogeny.