2.9 Positive selection analysis
The single-copy gene families of M. japonicus , L.
vannamei , P. monodon and F. chinensis , were used for the
positive selection analysis. MUSCLE (Edgar, 2004) was used to perform
multiple sequence alignment for protein sequences. A branch-site model
of CODEML in the PAML package (Yang, 2007) was used to detect positive
selection. The chi-squared test was used to calculate the P-value, which
was corrected using the false discovery rate (FDR).