Supplementary material for: nQMaker: estimating time non-reversible amino acid substitution models

Cuong Dang, Minh Bui, Hanon McShea, Joanna Masel, Jennifer James, Vinh Le & Robert Lanfear
Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly-used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this paper, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation...
1 citation reported since publication in 2022.
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