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

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()

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

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