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2matrix: A Utility For Indel Coding And Phylogenetic Matrix Concatenation, Nelson R. Salinas, Damon P. Little
2matrix: A Utility For Indel Coding And Phylogenetic Matrix Concatenation, Nelson R. Salinas, Damon P. Little
Publications and Research
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 …