2matrix: A utility for indel coding and phylogenetic matrix concatenation

View Researcher's Other Codes

Disclaimer: The provided code links for this paper are external links. Science Nest has no responsibility for the accuracy, legality or content of these links. Also, by downloading this code(s), you agree to comply with the terms of use as set out by the author(s) of the code(s).

Please contact us in case of a broken link from here

Authors Nelson R. Salinas, Damon P. Little
Journal/Conference Name International Journal of Plant Sciences
Paper Category , ,
Paper Abstract • Premise of the study Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel) events in sequence alignments and concatenate data sets. • Methods and Results A novel Perl script, 2matrix, was created to concatenate matrices of non-molecular characters and/or aligned sequences and to code indels. 2matrix outputs a variety of formats compatible with popular phylogenetic programs. • Conclusions 2matrix efficiently codes indels and concatenates matrices of sequences and non-molecular data. It is available for free download under a GPL (General Public License) open source license (https//github.com/nrsalinas/2matrix/archive/master.zip).
Date of publication 2014
Code Programming Language Perl
Comment

Copyright Researcher 2021