NAME

two-scalp.pl - Align or re-align sequences using various strategies

VERSION

version 0.231010

USAGE

    two-scalp.pl --in-seqs=<infiles>... [optional arguments]

REQUIRED ARGUMENTS

--in-seqs=<infiles>...

Path to input ALI file(s) with sequences to align. If only one file is specified, the script aligns all non-aligned sequences on the already aligned sequences (but see option --fam below). If several files are specified, each file is aligned on the previous one(s) in the given order.

OPTIONAL ARGUMENTS

--p-ref=<infile>

Path to input ALI file with already aligned sequences [default: none]. When such a master profile is specified, its sequences are only used as references for aligning the sequences of the other input file(s). Therefore, they will not appear in the final output.

--fam=<family>...

Family (or families) to consider when aligning sequences (already aligned or not) [default: none]. Families are processed in the given order, i.e., the first specified family is the first aligned and will serve as a master profile for the second one, etc. If sequences from additional families (or devoid of family) are also present, these are degapped and aligned on the profile obtained after aligning the specified families.

--keep-length

Alignment length remains unchanged when adding sequences from the same family [default: no]. This is achieved by clipping sequence regions not fitting in the existing alignment.

--linsi

Run mafft-linsi instead of the default mafft executable for more accurate alignment [default: no]. If the --keep-length option is specified, the default mafft will still be run when aligning sequences from the same family.

--threads=<n>

Number of threads to allocate to the aligner [default: n.default]. Mostly useful when the --linsi option is specified.

--out[-suffix]=<suffix>

Suffix to append to infile basename for deriving outfile name [default: suffix.default]. The infile giving the basename is the first given to --in-seqs.

--verbosity=<level>

Verbosity level for logging to STDERR [default: level.default]. Available levels range from 0 to 6. Level 6 corresponds to debugging mode.

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTORS

• Amandine BERTRAND <amandine.bertrand@doct.uliege.be>

• Valerian LUPO <valerian.lupo@doct.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.