Changelog

homologr v0.0.1

New functions:

• 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