NAME

idealize-ali.pl - Discard (nearly) gap-only sites from ALI files

VERSION

version 0.243430

USAGE

idealize-ali.pl <infiles> [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input ALI files [repeatable argument].

OPTIONAL ARGUMENTS

--max[-res-drop-site]=<n>

Number of non-gap character states allowed in a site to be dropped [default: 0]. When specified as a fraction between 0 and 1, it is interpreted as relative to the number of sequences in the ALI. By default, only shared gaps are dropped.

--keep-codons

When specified, this option forces the various applied masks to follow the codon structure [default: no]. This option only makes sense with nt seqs. See options --codon-max and --coding-frame for more control on this behavior.

--codon-max[-nt-drop]=<n>

Number of non-dropped nt sites allowed in a codon to be dropped [default: 1]. Allowed values are 0, 1 and 2. To be used when the option --keep-codons is also specified.

--coding-frame=<n>

Reading frame to be used when determining the ALI codon structure [default: +1]. Allowed values are -3 to -1 and +1 to +3. To be used when the option --keep-codons is also specified.

--out[-suffix]=<suffix>

Suffix to append to infile basenames for deriving outfile names [default: none]. When not specified, outfile names are taken from infiles but original infiles are preserved by being appended a .bak suffix.

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.