MOSAL is a program for computing the Pareto optimal alignments for the bicriteria pairwise sequence alignment. It allows the use of substitution matrices.
Support material for M.Abbasi, L. Paquete, A.Liefooghe, M. Pinheiro and P.Matias, Improvements on bicriteria pairwise sequence alignment: algorithms and applications, Bioinformatics, 29(8):996-1003, 2013.
Maintainer: Pedro Matias
This software is Copyright © 2013 M.Abbasi, L. Paquete, A.Liefooghe, M. Pinheiro and P.Matias.
This program is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 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 General Public License for more details.
Appropriate reference to this software should be made when describing research in which it played a substantive role, so that it may be replicated and verified by others. The bicriteria sequence alignment problem and the algorithms which this software implements are described in detail in . Please, mention the algorithm in the References section of your article. We would appreciate if you would email firstname.lastname@example.org with citations of papers referencing this work. MOSAL is distributed under the GNU General Public License.
Source code can be found here.
A limited version of the application is available online here.
In GNU/Linux, the program can be compiled from source by invoking
$ ./mosal seq1_file seq2_file [gaps|indels] [dp|dpp -b=NUMBER] [-ss=FILE] [--no-traceback]
||path to the 1st sequence file (FASTA format)|
||path to the 2nd sequence file (FASTA format)|
||use Dynamic Programming|
||use Dynamic Programming with pruning (need to specify -b=NUMBER)|
||use substitution score(ss) instead of #matches (path to the ss table)|
||specify the number of bounds for pruning version|
||output only the scores without the alignments|
|||M.Abbasi, L. Paquete, A.Liefooghe, M. Pinheiro and P.Matias, Improvements on bicriteria pairwise sequence alignment: algorithms and applications, Bioinformatics, 29(8):996-1003, 2013.|
|||L. Paquete, P. Matias, M. Abbasi, M. Pinheiro MOSAL: Software tools for multiobjective sequence alignment, Source Code for Biology and Medicine, 9(2), 2014.|