NAME

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

VERSION

version 0.180160

USAGE

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

REQUIRED ARGUMENTS

<infiles>

Path to input ALI files [repeatable argument].

OPTIONAL ARGUMENTS

--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.

# =item --mode=scratch|seqs2seqs|seqs2prof|prof2prof

# =item --coding-seqs # # Consider the nucleotide alignment as containing coding sequences [default: # no]. Currently, enabling this switch leads to using TBLASTX instead of BLASTN # when aligning sequences.

--coverage-mul=<n>

Coverage improvement required for aligning a new seq more than once [default: 1.1]. This means that if the BLAST alignment with the second template is at least 110% of the BLAST alignment with the first template, the new seq will be added twice to the ALI (under the ids *.H1.N and *.H2.N). Currently five templates are considered but this might change if needed.

--single-hsp

Ensure that a single HSP is aligned for each sequence [default: no]. When specified, only the best HSP of the template with the best coverage is retained in the alignment. In this case, a larger part of the sequence might be discarded. By default, more than one HSPs can be added and these have to be consolidated using an interactive alignment editor.

--verbosity=<level>

Verbosity level for logging to STDERR [default: 0]. 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>

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.