Bio-RNA-RNAaliSplit 0.03

Bio::RNA::RNAaliSplit is a distribution of Perl modules for splitting and
deconvoluting structural RNA multiple sequence alignments (MSA). 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 appliation is cleaning MSA from sequence that do
not fold into or prohibit folding into a common consensus structure.

This distribution is shipped with an executable script, RNAalisplit.pl,
which takes a RNA MSA in ClustalW format and performs the deconvolution.

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

R-scape (availavle from http://www.eddylab.org/R-scape) is used for
computing statistically significant covariation in base pairs.

Be sure to have all dependencies up and running on your system (and
available to the Perl interpreter) before continuing the installation
process.

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:

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

    AnnoCPAN, Annotated CPAN documentation
        http://annocpan.org/dist/Bio-RNA-RNAaliSplit

    CPAN Ratings
        http://cpanratings.perl.org/d/Bio-RNA-RNAaliSplit

    Search CPAN
        http://search.cpan.org/dist/Bio-RNA-RNAaliSplit


LICENSE AND COPYRIGHT

Copyright (C) 2017 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/>.

