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.