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 a...