2.8 | Expansion and contraction of gene family
We used CAFE (v 2.0, De et al. 2006) to infer gene family sizes of the
most recent common ancestor (MRCA) and to analyze expansion and
contraction of gene family based on the phylogenetic tree.
2.9
| Positively selected gene analysis
Codeml (Schabauer et al. 2012) software implemented in the PAML program
package was used to identify positively selected genes in the assembled
Sulv 1 genome with a branch model (model=2, NSsites=0). The positively
selected genes were annotated by GO and KEGG analyses.