Enveomics collection

ogs.rb

Identifies Orthology Groups (OGs) in Reciprocal Best Matches (RBM) between all pairs in a collection of genomes.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

§ Arguments

Out*

 --out out_file  Output file containing the detected OGs.

Dir

 --dir in_dir  Directory containing the RBM files.

Required unless --pre-ogs is passed.

Pre ogs

 --pre-ogs in_file  Pre-computed OGs file(s), separated by commas.

Unchecked

 --unchecked   Do not check internal redundancy in OGs.

Format

 --format string  Format of the filenames for the RBM files (within -d), using regex syntax.

Quiet

 --quiet   Run quietly (no STDERR output).