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ReplacementMatrix: a Web Server for Maximum Likelihood Estimation of Amino Acid Replacement Rate Matrices

Cao Cuong Dang 1 Vincent Lefort 2 Vinh Le 1 Quang Le Si 3 Olivier Gascuel 2, *
* Corresponding author
2 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Amino acid replacement rate matrices are an essential basis of protein studies (e.g. in phylogenetics and alignment). A number of general purpose matrices have been proposed (e.g. JTT, WAG, LG) since the seminal work of Margaret Dayhoff and co-workers. However, it has been shown that matrices specific to certain protein groups (e.g. mitochondrial) or life domains (e.g. viruses) differ significantly from general average matrices, and thus perform better when applied to the data to which they are dedicated. This Web server implements the maximum-likelihood estimation procedure that was used to estimate LG, and provides a number of tools and facilities. Users upload a set of multiple protein alignments from their domain of interest and receive the resulting matrix by email, along with statistics and comparisons with other matrices. A non-parametric bootstrap is performed optionally to assess the variability of replacement rate estimates. Maximum-likelihood trees, inferred using the estimated rate matrix, are also computed optionally for each input alignment. Finely tuned procedures and up-to-date ML software (PhyML 3.0, XRATE) are combined to perform all these heavy calculations on our clusters.
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Submitted on : Tuesday, November 29, 2011 - 7:24:10 PM
Last modification on : Wednesday, May 13, 2020 - 3:28:01 PM
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Cao Cuong Dang, Vincent Lefort, Vinh Le, Quang Le Si, Olivier Gascuel. ReplacementMatrix: a Web Server for Maximum Likelihood Estimation of Amino Acid Replacement Rate Matrices. Bioinformatics, Oxford University Press (OUP), 2011, 27 (19), pp.2758-2760. ⟨lirmm-00646393⟩

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