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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135906 | PMC |
| http://dx.doi.org/10.3389/fmicb.2018.02065 | DOI Listing |
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BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more.
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Lewis B. and Dorothy Cullman Program for Molecular Systematics The New York Botanical Garden, Bronx New York USA.
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.
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