- adding
diamond_best_hits(): Perform a DIAMOND best hit search - adding
diamond_reciprocal_best_hits(): Perform a DIAMOND best reciprocal hit search - adding
filter_best_hits(): Helper function to select best DIAMOND hit based on minimum evalue - adding
codon_aln(): Codon Alignments using PAL2NAL - adding
dnds(): Genome-wide pairwise inference of synonymous versus non-synonymous substitution rates (dnds) - adding
dnds_across_multiple_species(): Genome-wide pairwise inference of synonymous versus non-synonymous substitution rates (dnds) across multiple subject organisms - adding
import_cds(): Import the coding sequences from a fasta file - adding
import_dnds_across_multiple_species(): Import 'dnds' tables by gene locus and splice varaint for a set of species - adding
import_proteome(): Import protein sequences from a 'fasta' file - adding
internal_dnds(): Internal dnds computations - adding
pairwise_aln(): Pairwise Global Sequence Alignments - adding
substitutionrate(): Internal function for dNdS computations - adding
dnds_across_multiple_species_plot(): Plot pairwise dN, dS, or dN/dS distributions of orthologous genes across species