Enveomics collection

ogs.mcl.rb

Identifies Orthology Groups (OGs) in Reciprocal Best Matches (RBM) between all pairs in a collection of genomes, using the Markov Cluster Algorithm.

    See source code, Artistic license 2.0.

§ References

    Enright et al, 2002, NAR; 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.

Mandatory, unless --abc is set to a non-empty file.

Format

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

Inflation

 --inflation float  Inflation parameter for MCL clustering.

Blind

 --blind   If set, computes clusters without taking bitscore into account.

Evalue

 --evalue   If set, uses the e-value to weight edges, instead of the default Bit-Score.

Identity

 --identity   If set, uses the identity to weight edges, instead of the default Bit-Score.

Best match

 --best-match   If set, it assumes best-matches instead reciprocal best matches.

Mcl bin

 --mcl-bin in_dir  Path to the directory containing the mcl binaries. By default, assumed to be in the PATH.

abc

 --abc out_file  Use this abc file instead of a temporal file.

Threads

 --threads integer  Number of threads to use.

Quiet

 --quiet   Run quietly (no STDERR output).