Pipeline method flow chart

Fig.1: Flow chart of Fishing Gene Family. The flow chart mainly involved two parts. The fist step is paralogous search through which define the gene family, using blast get candidate homologs from genome and do accurate alignment GeneWise, from GeneWise result get useful information such as copy position and intron/exon structure; The second step is evolutionary analysis. We calculate the Ka/Ks ratio of each duplication to their nearest parental copy, check stop codon and frame shift truncations to judge duplication fate and draw the phylogenetic tree using TreeFam method.