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