Function reference • orthologr

All functions
`blast()`	Perform a BLAST+ search
`blast_best()`	Perform a BLAST+ best hit search
`blast_rec()`	Perform a BLAST+ reciprocal best hit (RBH) search
`cds2aa()`	Translate CDS file to Amino Acids file
`check_annotation()`	Check whether an annotation file contains outlier lines
`clean_all_folders()`	Delete the internal folder hierarchy
`codon_aln()`	Compute a Codon Alignment
`compute_dnds()`	Compute dNdS Values For A Given Pairwise Alignment
`dNdS()`	Compute dNdS values for two organisms
`diamond()`	Perform a DIAMOND2 search
`diamond_best()`	Perform a DIAMOND2 best hit search
`diamond_rec()`	Perform a DIAMOND2 reciprocal best hit (RBH) search
`divergence_map()`	Sort dNdS Values Into Divergence Strata
`divergence_stratigraphy()`	Perform Divergence Stratigraphy
`extract_features()`	Helper function to extract gene loci and splice variant IDs from GFF files
`filter_best_hits()`	Helper function to select best BLAST hit based on minimum evalue
`filter_core_set()`	Helper function to extract a core set of orthologous gene loci
`filter_core_set_lnc()`	Helper function to extract a core set of orthologous lncRNAs
`filter_dNdS()`	Filter dNdS values
`generate_ortholog_tables()`	Generate ortholog tables by gene locus and splice varaint
`generate_ortholog_tables_all()`	Generate ortholog tables by gene locus and splice varaint for a set of species
`import_ortholog_tables_all()`	Importing output pairwise orthologs tables generated with `generate_ortholog_tables_all`
`lnc_map_core_orthologs()`	Retrieve a core set of orthologous lncRNAs from the pairwise lncRNA orthologs map
`lnc_map_counts()`	Count number of orthologous lncRNAs per pairwise species comparison
`map_generator_dnds()`	Generate dNdS Maps Between a Query Organism and Multiple Subject Organisms
`map_generator_lnc()`	Infer orthologous lncRNAs between multiple species
`multi_aln()`	Compute Multiple Sequence Alignments
`orthofinder2()`	Interface function to Orthofinder2
`orthofinder2_retrieve_core_orthologs()`	Retrieve core orthologs across multiple species from Orthofinder2 output
`orthologs()`	Main Orthology Inference Function
`orthologs_lnc()` `orthologs_lnc()`	Orthology Inference of lncRNAs
`pairwise_aln()`	Compute Pairwise Alignments
`plot_diverse_homology_thresholds()`	Diverse line plots visualizing the number of pairwise orthologs within a ortho table generated with `generate_ortholog_tables_all` based on different sets of homology thresholds.
`plot_diverse_homology_thresholds_core_orthologs()`	Diverse line plots visualizing the number of core orthologs within a ortho table generated with `generate_ortholog_tables_all` based on different sets of homology thresholds.
`plot_pairwise_orthologs()`	A line plot visualizing the number of pairwise orthologs within a ortho table generated with `generate_ortholog_tables_all`
`promotor_divergence_estimation()`	Estimate the DNA distance between promotor sequences
`promotor_divergence_of_orthologous_genes()`	Compute promotor sequence divergence of orthologous genes
`read.cds()`	Read the CDS of a given organism
`read.dnds.tbl()`	Import a dNdS table generated with `dNdS`
`read.genome()`	Read the genome of a given organism
`read.proteome()`	Read the proteome of a given organism
`retrieve_core_orthologs()`	Retrieve a core set of orthologous gene loci from several pairwise ortholog tables
`retrieve_longest_isoforms()`	Retrieve the longest isoforms from a proteome file and save results as fasta file
`retrieve_longest_isoforms_all()`	Retrieve the longest isoforms of several proteome files stored in a folder
`select_orthologs()`	Select orthologs based on either gene locus or splice variant
`set_blast()`	Create a BLASTable database with makeblastdb
`set_diamond()`	Create a DIAMONDable database with `diamond makedb`
`substitutionrate()`	Internal function for dNdS computations
`testCoreOrthoParamsGeneLocus()`	Helper function for `plot_diverse_homology_thresholds_core_orthologs`
`testCoreOrthoParamsSpliceVariant()`	Helper function for splice variant based `plot_diverse_homology_thresholds_core_orthologs`
`transl()`	Translate DNA to Amino Acids
`translate_cds_to_protein()`	Translate coding sequences into amino acid sequences
`translate_cds_to_protein_all()`	Translate coding sequences into amino acid sequences for multiple files
`write.proteome()`	Save a proteome in fasta format

Reference

All functions