cds_scerevisiae         Coding sequences (CDS) of S. cerevisiae
classify_gene_pairs     Classify duplicate gene pairs based on their
                        modes of duplication
classify_genes          Classify genes into unique modes of duplication
classify_ssd_pairs      Classify small-scale duplication-derived gene
                        pairs into subcategories
diamond_inter           Interspecies DIAMOND output for yeast species
diamond_intra           Intraspecies DIAMOND output for S. cerevisiae
find_ks_peaks           Find peaks in a Ks distribution with Gaussian
                        Mixture Models
get_anchors_list        Get a list of anchor pairs for each species
get_transposed          Get transposed duplicate pairs
get_wgd_pairs           Get gene pairs derived from whole-genome and
                        small-scale duplications
gmax_ks                 Duplicate pairs and Ks values for Glycine max
pairs2kaks              Calculate Ka, Ks, and Ka/Ks from duplicate gene
                        pairs
plot_ks_peaks           Plot histogram of Ks distribution with peaks
scerevisiae_kaks        Duplicate pairs and Ka, Ks, and Ka/Ks values
                        for S. cerevisiae
split_pairs_by_peak     Split gene pairs based on their Ks peaks
yeast_annot             Genome annotation of the yeast species S.
                        cerevisiae and C. glabrata
yeast_seq               Protein sequences of the yeast species S.
                        cerevisiae and C. glabrata
