ATGC: Replacement Matrix

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.

Paper

Replacement Matrix:

"A web server for maximum likelihood estimation of amino acid replacement rate matrix."

Dang C.C., Lefort V., Le V.S., Le Q.S., Gascuel O.

Bioinformatics. 2011, 27(19):2758-60.

Related papers

FLU model:

"FLU, an amino acid substitution model for influenza proteins."

Dang C.C., Le Q.S., Gascuel O., Le V.S.

BMC Evolutionary Biology, 10:99, 2010.
PhyML 3.0:

"New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0."

Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.

Systematic Biology, 59(3):307-21, 2010.
LG model:

"An Improved General Amino-Acid Replacement Matrix."

Le S.Q., Gascuel O.

Molecular Biology and Evolution, 25(7):1307-20, 2008.
XRate:

"a fast prototyping, training and annotation tool for phylo-grammars."

Klosterman P.S., Uzilov A.V., Bendaña Y.R., Bradley R.K., Chao S., Kosiol C., Goldman N., Holmes I.

BMC Bioinformatics, 7:428, 2006.

Contacts

For any question about the algorithm, the program options, please contact:

Olivier Gascuel (author)
LIRMM, Montpellier, France.
Vincent Lefort
LIRMM, Montpellier, France.