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DOE OSTI · 2480577

BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

Salinas, Nelson R.·Eshel, Gil·Coruzzi, Gloria M.·DeSalle, Rob·Tessler, Michael·Little, Damon P.
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Abstract

Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program. BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data. The script works in UNIX-like environments (e.g., LINUX, MacOS, Windows Subsystem for LINUX).

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59 BASIC BIOLOGICAL SCIENCESconcatenationgene contentgene presence/absenceindel codingmorphologyoccupancy filteringphylogenomicsreduced amino acid alphabets

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Salinas, Nelson R., Eshel, Gil, Coruzzi, Gloria M., DeSalle, Rob, Tessler, Michael, Little, Damon P.. 2024-09-24. BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more. https://doi.org/10.1002/aps3.11604

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