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Table 1 Brief description of models: Amino acid substitution models

From: Superiority of a mechanistic codon substitution model even for protein sequences in Phylogenetic analysis

mtREV-dGmr, cpREV64-dGmr, FLU-dGmr,

The empirical amino acid rates of mtREV [6], cpREV64 [28], and FLU [29] are employed.

JTT-F-dGmr, WAG-F-dGmr, LG-F-dGmr,mtREV-F-dGmr, cpREV10-F-dGmr,cpREV64-F-dGmr, FLU-F-dGmr

The empirical amino acid exchangeabilities of JTT [5], WAG [10], LG [11], mtREV [6], cpREV10 [8], cpREV64 [28], and FLU [29] are employed. The suffix "-F" means that equilibrium amino acid frequencies are assumed to be equal to those of amino acid sequences.

  1. The suffix "-dGmr" means that the variation of substitution rate is approximated by a discrete gamma distribution [38] with m categories of unequal probabilities; see Additional file 1 for details.
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BMC Ecology and Evolution

ISSN: 2730-7182

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