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

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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

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