2matrix: A Utility for Indel Coding and Phylogenetic Matrix Concatenation
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...
| Main Authors: | , |
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| Formato: | Artigo |
| Idioma: | English |
| Publicado em: |
Wiley
2014-01-01
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| Colecção: | Applications in Plant Sciences |
| Assuntos: | |
| Acesso em linha: | http://www.bioone.org/doi/full/10.3732/apps.1300083 |
| Resumo: | 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). |
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| ISSN: | 2168-0450 |