2matrix: A utility for indel coding and phylogenetic matrix concatenation1. (7th January 2014)

• Record Type: Journal Article
• Authors: Salinas, Nelson R.; Little, Damon P.
• Is Part Of: Applications in plant sciences. Volume 2:Number 1(2014)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2014-01-07
• Subjects: 2matrix -- file conversion -- indel coding -- software; Plants -- Periodicals; Plant physiology -- Periodicals; Plant Physiological Phenomena; Plant physiology; Plants; Periodicals; Periodicals; Fulltext; Internet Resources; Periodicals; 580
• DOI: 10.3732/apps.1300083
• Languages: English
• ISSNs: 2168-0450

Abstract

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 ).