DOAJ Open Access 2024

BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

Nelson R. Salinas Gil Eshel Gloria M. Coruzzi Rob DeSalle Michael Tessler +1 lainnya

Abstrak

Abstract Premise 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. Methods and Results 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). Conclusions BAD2matrix helps simplify phylogenomic pipelines and can be downloaded from https://github.com/dpl10/BAD2matrix/tree/master under a GNU General Public License v2.

Topik & Kata Kunci

Biology (General) Botany

Penulis (6)

Nelson R. Salinas

Gil Eshel

Gloria M. Coruzzi

Rob DeSalle

Michael Tessler

Damon P. Little

Format Sitasi

APA MLA BibTeX

Salinas, N.R., Eshel, G., Coruzzi, G.M., DeSalle, R., Tessler, M., Little, D.P. (2024). BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more. https://doi.org/10.1002/aps3.11604

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Informasi Jurnal

Tahun Terbit: 2024
Sumber Database: DOAJ
DOI: 10.1002/aps3.11604
Akses: Open Access ✓