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check_annotation_file_completeness()
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Check whether an annotation file contains outlier lines |
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codon_aln()
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Codon Alignments using PAL2NAL |
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diamond_best_hits()
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Perform a DIAMOND best hit search |
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diamond_reciprocal_best_hits()
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Perform a DIAMOND best reciprocal hit search |
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dnds()
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Genome-wide pairwise inference of synonymous versus non-synonymous substitution rates (dnds) |
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dnds_across_multiple_species()
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Genome-wide pairwise inference of synonymous versus non-synonymous substitution rates (dnds) across multiple subject organisms |
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dnds_across_multiple_species_plot()
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Plot pairwise dN, dS, or dN/dS distributions of orthologous genes |
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extract_features()
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Helper function to extract gene loci and splice variant IDs from GFF files |
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filter_best_hits()
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Helper function to select best DIAMOND hit based on minimum evalue |
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import_cds()
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Import the coding sequences from a fasta file |
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import_dnds_across_multiple_species()
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Import dnds tables by gene locus and splice varaint for a set of species |
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import_dnds_tbl()
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Import a dnds table generated with dnds |
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import_proteome()
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Import protein sequences from a fasta file |
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internal_dnds()
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Internal dnds computations |
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internal_import_dnds_across_multiple_species()
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Generate ortholog tables by gene locus and splice varaint |
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pairwise_aln()
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Pairwise Global Sequence Alignments |
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select_best_splice_variants()
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Select best splice variant representing orthologous gene loci |
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substitutionrate()
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Internal function for dNdS computations |
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transl()
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Translate DNA to Amino Acids |
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transl_cds_to_aa()
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Translate CDS file to Amino Acids file |