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
diamond_inter           Interspecies DIAMOND output for yeast species
diamond_intra           Intraspecies DIAMOND output for S. cerevisiae
duplicates2counts       Get a duplicate count matrix for each genome
find_ks_peaks           Find peaks in a Ks distribution with Gaussian
                        Mixture Models
fungi_kaks              Duplicate pairs and Ka, Ks, and Ka/Ks values
                        for fungi species
get_anchors_list        Get a list of anchor pairs for each species
get_intron_counts       Get a data frame of intron counts per gene
get_segmental           Classify gene pairs derived from segmental
                        duplications
get_tandem_proximal     Classify gene pairs derived from tandem and
                        proximal duplications
get_transposed          Classify gene pairs originating from
                        transposon-derived duplications
get_transposed_classes
                        Classify TRD genes as derived from either DNA
                        transposons or retrotransposons
gmax_ks                 Duplicate pairs and Ks values for Glycine max
pairs2kaks              Calculate Ka, Ks, and Ka/Ks from duplicate gene
                        pairs
plot_duplicate_freqs    Plot frequency of duplicates per mode for each
                        species
plot_ks_distro          Plot distribution of synonymous substitution
                        rates (Ks)
plot_ks_peaks           Plot histogram of Ks distribution with peaks
plot_rates_by_species   Plot distributions of substitution rates (Ka,
                        Ks, or Ka/Ks) per species
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
