ali2phylip.pl - Convert (and filter) ALI files to PHYLIP files for tree building
ali2phylip.pl <infiles> [optional arguments]
Path to main outfile collecting statistics for all infiles [default: none]. When specified, the script does not produce any outfile but instead reports statistics in a tabular output suitable to further analysis in R. This option is useful for evaluating the effects of various parameter settings. It overrides all the options pertaining to outfiles.
Consider the input ALI file as generated by SCaFoS [default: no]. Currently, specifying this option results in turning all ambiguous and missing character states to gaps.
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. To completely disable deletion of shared gaps, use -1.
Stringency of the Gblocks mask to be applied [default: none]. The following modes are available: strict, medium and loose. This option requires to have a
Gblocksexecutable in the
Stringency of the BMGE mask to be applied [default: none]. The following modes are available: strict, medium and loose. This option requires to have a
bmge.shscript in the
bmge.shscript should be as follows:
#!/bin/sh java -jar path-to-bmge/BMGE.jar -i $1 -t $2 -h $3 -g $4 -oh $5
Apply a simple parsimony mask where only parsimony-informative sites are retained [default: no].
Number of known character states required by a sequence for it to be exported [default: 0]. When specified as a fraction between 0 and 1, it is interpreted as relative to the longest ungapped sequence of the ALI. Note that this optional filtering step takes place after the optional Gblocks-based masking step.
Delete constant sites just as the
-dcoption of PhyloBayes [default: no].
Sequence id mapping switch [default: no]. When specified, sequence ids are renamed to 'seqN' and IDM files are created. Enabling this option is highly recommended when exporting to PHYLIP.
Output file in P80 format instead of PHYLIP [default: no]. This option is useful for keeping full-length ids without mapping.
Output file in ALI format instead of PHYLIP [default: no]. This option is useful for generating filtered ALI files usable by SCaFoS.
Print the usual program information
Denis BAURAIN <firstname.lastname@example.org>
Arnaud DI FRANCO <email@example.com>
Raphael LEONARD <firstname.lastname@example.org>
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.