Amino Acid Substitution Matrices Estimated by Maximum Likelihood
Genome Informatics (2001)
Available from citeseerx.ist.psu.edu
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Abstract
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
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