BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

• Published in: Applications in plant sciences Vol. 12; no. 6; pp. e11604 - n/a
• Main Authors: Salinas, Nelson R., Eshel, Gil, Coruzzi, Gloria M., DeSalle, Rob, Tessler, Michael, Little, Damon P.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.11.2024; Botanical Society of America; John Wiley and Sons Inc; Wiley
• Subjects: Amino acids; BASIC BIOLOGICAL SCIENCES; computer software; concatenation; Datasets; DNA; gene content; Gene deletion; gene presence/absence; Genes; indel coding; Missing data; Morphology; Names; Nucleotide sequence; occupancy filtering; Phylogenetics; phylogenomics; reduced amino acid alphabets; Software Note; gene content; concatenation; morphology; indel coding; reduced amino acid alphabets; occupancy filtering; phylogenomics; gene presence/absence
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11604

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.