Package index

Sequence Search (`DIAMOND2`)

Run DIAMOND2 homology searches and build DIAMOND databases.

diamond(): Perform a DIAMOND2 search
diamond_best(): Perform a DIAMOND2 best hit search
diamond_rec(): Perform a DIAMOND2 reciprocal best hit (RBH) search
set_diamond(): Create a DIAMONDable database with diamond makedb

Sequence Search (BLAST+)

Run BLAST+ homology searches, filter hits, and build BLAST databases.

blast(): Perform a BLAST+ search
blast_best(): Perform a BLAST+ best hit search
blast_rec(): Perform a BLAST+ reciprocal best hit (RBH) search
set_blast(): Create a BLASTable database with makeblastdb
filter_best_hits(): Helper function to select best BLAST hit based on minimum evalue

Sequence Alignment

Pairwise and multiple sequence alignments, including codon-aware alignments.

pairwise_aln(): Compute Pairwise Alignments
multi_aln(): Compute Multiple Sequence Alignments
codon_aln(): Compute a Codon Alignment

Orthology Inference

Infer orthologous genes between pairs or sets of species.

orthologs(): Main Orthology Inference Function
select_orthologs(): Select orthologs based on either gene locus or splice variant

Sequence Clustering

Cluster sequences with diamond deepclust and post-process clusters.

deepclust(): Cluster sequences using diamond deepclust
deepclust_annotate(): Annotate deepclust output with source file metadata
deepclust_realign(): Realign sequences within deepclust clusters

dNdS / Substitution Rates

Compute, filter, and import pairwise synonymous (dS) and non-synonymous (dN) substitution rates, and generate multi-species dNdS maps.

dNdS(): Compute dNdS values for two organisms
compute_dnds(): Compute dNdS Values For A Given Pairwise Alignment
substitutionrate(): Internal function for dNdS computations
filter_dNdS(): Filter dNdS values
read.dnds.tbl(): Import a dNdS table generated with dNdS
map_generator_dnds(): Generate dNdS Maps Between a Query Organism and Multiple Subject Organisms

Divergence Stratigraphy

Perform divergence stratigraphy to assign genes to evolutionary divergence strata based on dNdS values.

divergence_stratigraphy(): Perform Divergence Stratigraphy
divergence_map(): Sort dNdS Values Into Divergence Strata

Core Ortholog Tables

Generate, retrieve, and import pairwise and multi-species ortholog tables.

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
retrieve_core_orthologs(): Retrieve a core set of orthologous gene loci from several pairwise ortholog tables
filter_core_set(): Helper function to extract a core set of orthologous gene loci

OrthoFinder2 Interface

Run OrthoFinder2 and retrieve core orthologs from its output.

orthofinder2(): Interface function to Orthofinder2
orthofinder2_retrieve_core_orthologs(): Retrieve core orthologs across multiple species from Orthofinder2 output

lncRNA Orthology

Infer orthologous long non-coding RNAs (lncRNAs) and summarise results.

orthologs_lnc(): Orthology Inference of lncRNAs
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_lnc(): Infer orthologous lncRNAs between multiple species
filter_core_set_lnc(): Helper function to extract a core set of orthologous lncRNAs

Promoter Divergence

Estimate divergence of promoter sequences for orthologous genes.

promotor_divergence_estimation(): Estimate the DNA distance between promotor sequences
promotor_divergence_of_orthologous_genes(): Compute promotor sequence divergence of orthologous genes

Visualization

Plot ortholog counts and homology-threshold curves across species comparisons.

plot_pairwise_orthologs(): A line plot visualizing the number of pairwise orthologs within a ortho table generated with generate_ortholog_tables_all
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.
testCoreOrthoParamsGeneLocus(): Helper function for plot_diverse_homology_thresholds_core_orthologs
testCoreOrthoParamsSpliceVariant(): Helper function for splice variant based plot_diverse_homology_thresholds_core_orthologs

Sequence I/O

Read and write genome, proteome, and CDS files.

read.genome(): Read the genome of a given organism
read.proteome(): Read the proteome of a given organism
read.cds(): Read the CDS of a given organism
write.proteome(): Save a proteome in fasta format

Sequence Processing

Translate CDS sequences and retrieve longest isoforms from proteome files.

transl(): Translate DNA to Amino Acids
cds2aa(): Translate CDS file to Amino Acids file
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
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

Annotation Utilities

Check annotation files, extract gene loci / splice variant features from GFF files, and manage internal folder structure.

check_annotation(): Check whether an annotation file contains outlier lines
extract_features(): Helper function to extract gene loci and splice variant IDs from GFF files
clean_all_folders(): Delete the internal folder hierarchy

Sequence Search (DIAMOND2)