Bio-RNA-RNAaliSplit 0.09

Bio::RNA::RNAaliSplit is a distribution of Perl modules for splitting
and deconvoluting structural RNA multiple sequence alignments
(MSAs). Its primary purpose is to partition a MSA into subsets of
sequences that have a common consensus structure which is different
from the consesus structure of the other set. Another application is
cleaning MSAs from sequence that do not fold into or prohibit folding
into a common consensus structure.

This distribution is shipped with a set of executables within the
'scripts' folder. RNAalisplit.pl, takes a RNA MSA in ClustalW format
and performs the deconvolution. The eval_alignment.pl executable is a
lightweight evaluator for structural alignments of RNA.

THIRD PARTY DEPENDENCIES

This module depends heavily on third party RNA bioinformatics software.

It requires the ViennaRNA Package v2.3.4 or above (available from
http://www.tbi.univie.ac.at/RNA ). Specifically, the 'RNAalifold',
'AnalyseDists' executables as well as the RNA Perl module shipped with
ViennaRNA are used by RNAaliSplit.

RNAz v2.1 (availale from http://www.tbi.univie.ac.at/~wash/RNAz) is
used for classification of split subalignments.

R-scape v1.2.2 or above is used for computing statistically
significant covariation in base pairs. Download R-scape from
http://www.eddylab.org/R-scape .

Be sure to have all dependencies up and running on your system (and
available to the Perl interpreter) priot to installation of
Bio::RNA::RNAaliSplit.

INSTALLATION

To install this module, run the following commands:

	perl Makefile.PL
	make
	make test
	make install

SUPPORT AND DOCUMENTATION

After installing, you can find documentation for this module with the
perldoc command.

    perldoc Bio::RNA::RNAaliSplit

You can also look for information at:

    metaCPAN
        https://metacpan.org/release/Bio-RNA-RNAaliSplit

    RT, CPAN's request tracker (report bugs here)
        http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-RNA-RNAaliSplit

LICENSE AND COPYRIGHT

Copyright (C) 2017-2019 Michael T. Wolfinger

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU Affero General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public
License along with this program.  If not, see
L<http://www.gnu.org/licenses/>.

