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Article

Superiority of a mechanistic codon substitution model even for protein sequences in phylogenetic analysis.

BMC evolutionary biology - 21 Nov 2013

Miyazawa Sanzo

Abstract excerpt

BACKGROUND: Nucleotide and amino acid substitution tendencies are characteristic of each species, organelle, and protein family. Hence, various empirical amino acid substitution rate matrices have needed to be estimated for phylogenetic analysis: JTT, WAG, and LG for nuclear proteins, mtREV for mitochondrial proteins, cpREV10 and cpREV64 for chloroplast-encoded proteins, and FLU for influenza proteins. On the...

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PMID: 24256155
DOI: 10.1186/1471-2148-13-257
PMCID: PMC4225520

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