The present work describes protrates, a program that estimates amino acid substitution matrices and among-site substitution rates based on their likelihood for a given tree topology and a dataset of aligned proteins. The issue of producing maximum likelihood (ML) rate matrices over protein data have been adressed under the framework of general-purpose unbiased substitution matrices [1, 9], since it's believed that parsimony-estimated matrices can be systematically distorted and ignore backward and parallel substitutions - which can affect branch lenghts of ML topologies [
CITATION STYLE
Leonardo de Oliveira Martins, & Zanotto, P. M. D. A. (2001). Amino Acid Substitution Matrices Estimated by Maximum Likelihood. GENOME INFORMATICS SERIES. Retrieved from http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.96.1716&rep=rep1&type=pdf
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