Name
Title | ||
|---|---|---|
ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices. |
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 coworkers. 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 nonparametric 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. |
Year | DOI | Venue |
|---|---|---|
2011 | 10.1093/bioinformatics/btr435 | BIOINFORMATICS |
Field | DocType | Volume |
Data mining,General purpose,Amino acid replacement,Computer science,Matrix (mathematics),Upload,Maximum likelihood,Software,Bioinformatics,Nonparametric bootstrap,Web server | Journal | 27 |
Issue | ISSN | Citations |
19 | 1367-4803 | 1 |
PageRank | References | Authors |
0.37 | 2 | 5 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Cuong Cao Dang | 1 | 6 | 1.41 |
| Vincent Lefort | 2 | 4 | 1.80 |
| Vinh Sy Le | 3 | 41 | 9.52 |
| Si Quang Le | 4 | 57 | 5.94 |
| Olivier Gascuel | 5 | 433 | 76.01 |