Enveomics collection

Aln.cat.rb

Concatenates several multiple alignments in FastA format into a single multiple alignment. The IDs of the sequences (or the ID prefixes, if using --ignore-after) must coincide across files.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

§ Arguments

Coords

 --coords out_file  Output file of coordinates in RAxML-compliant format.

Ignore after

 --ignore-after string  Remove everything in the IDs after the specified string.

Remove invariable

 --remove-invariable   Remove invariable sites.

Invariable sites are defined as columns with only one state and undefined characters. Additional ambiguous characters may exist and should be declared using --undefined.

Missing char

 --missing-char character  Character denoting missing data.

Model

 --model string  Name of the model to use if --coords is used.

See RAxML's documentation for additional information.

Undefined

 --undefined string  All characters to be regarded as 'undefined'. It should include all ambiguous and missing data chars. Ignored unless --remove-invariable.

Quiet

 --quiet   Run quietly (no STDERR output).

Input alignments*

 in_file  Input alignments in FastA format.

Output alignment*

 out_file  Output concatenated alignment.