BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

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

doi:10.1002/aps3.11604

BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

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

Biology and Genomics

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Article number	e11604
Journal	Applications in Plant Sciences
Volume	12
Issue number	6
DOIs	https://doi.org/10.1002/aps3.11604
State	Published - Nov 1 2024

Keywords

concatenation
gene content
gene presence/absence
indel coding
morphology
occupancy filtering
phylogenomics
reduced amino acid alphabets

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Plant Science

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10.1002/aps3.11604

Cite this

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title = "BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more",

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.",

keywords = "concatenation, gene content, gene presence/absence, indel coding, morphology, occupancy filtering, phylogenomics, reduced amino acid alphabets",

author = "Salinas, {Nelson R.} and Gil Eshel and Coruzzi, {Gloria M.} and Rob DeSalle and Michael Tessler and Little, {Damon P.}",

note = "Publisher Copyright: {\textcopyright} 2024 The Author(s). Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.",

year = "2024",

month = nov,

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doi = "10.1002/aps3.11604",

language = "English (US)",

volume = "12",

journal = "Applications in Plant Sciences",

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AU - Salinas, Nelson R.

AU - Eshel, Gil

AU - Coruzzi, Gloria M.

AU - DeSalle, Rob

AU - Tessler, Michael

AU - Little, Damon P.

PY - 2024/11/1

Y1 - 2024/11/1

N2 - 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.

AB - 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.

KW - concatenation

KW - gene content

KW - gene presence/absence

KW - indel coding

KW - morphology

KW - occupancy filtering

KW - phylogenomics

KW - reduced amino acid alphabets

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BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more

Abstract

Keywords

ASJC Scopus subject areas

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