Maximum likelihood estimation of amino acid replacement rate matrix

Cuong Cao Dang, Vincent Lefort, Vinh Sy Le, Quang Si Le, and Olivier Gascuel.
Bioinformatics. 2011, 27(19):2758-60.

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Input alignments
in an archive (.zip or .gz)
FASTA format PHYLIP format
Initial matrix (PAML format) File LG matrix
Compute PhyML trees using estimated matrix yes no
Estimate variability of rate estimates (run 10 bootstrap replicates) yes no

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