Enveomics collection

HMM.haai.rb

Estimates Average Amino Acid Identity (AAI) from the essential genes extracted and aligned by HMM.essential.rb (see Alignments).

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

HMM.haai.rb [opts]

§ Arguments

Alignments 1

 -1 in_file  Input alignments file for genome 1.

Alignments 2

 -2 in_file  Input alignments file for genome 2.

Alignment output

 --aln-out out_file  Output file containing the aligned proteins.

Components

 --components out_file  Output file containing the components of the estimation. Tab-delimited file with model name, matches, and columns.

Quiet

 --quiet   Run quietly (no STDERR output).

* Mandatory.