title: ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  http://www.atgc-montpellier.fr/ReplacementMatrix/
  
  
  BACKGROUND
  olivier.gascuel@lirmm.fr
  
  
  BACKGROUND
  Supplementary data are available at http://www.atgc-montpellier.fr/ReplacementMatrix/
authors.affiliation: College of Technology and Information Technology Institute, Vietnam National University, Hanoi, Vietnam.
authors.forename: Cuong Cao
authors.initials: CC
authors.lastname: Dang
authors.forename: Vincent
authors.initials: V
authors.lastname: Lefort
authors.forename: Vinh Sy
authors.initials: VS
authors.lastname: Le
authors.forename: Quang Si
authors.initials: QS
authors.lastname: Le
authors.forename: Olivier
authors.initials: O
authors.lastname: Gascuel
mesh_terms: D000596:Amino Acids / Q000235:genetics*; D020407:Internet; D016013:Likelihood Functions; D010802:Phylogeny; D011336:Probability; D011506:Proteins / Q000235:genetics; D016415:Sequence Alignment / Q000706:statistics & numerical data*; D012984:Software
chemical_list: D000596:Amino Acids; D011506:Proteins