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Protocols

XRate specifications

Information


Unique identifier OMICS_22811
Name XRate
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
gcc, make, ar
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Ian H Holmes
  • person_outline Peter Klosterman
  • person_outline Andrew Uzilov
  • person_outline Yuri Bendana
  • person_outline Robert Bradley

Additional information


https://biowiki.org/wiki/index.php/Xrate_Tutorial

Publication for XRate

XRate citations

 (10)
library_books

Solving the master equation for Indels

2017
BMC Bioinformatics
PMCID: 5427538
PMID: 28494756
DOI: 10.1186/s12859-017-1665-1

[…] [], and Hasegawa et al. [], among others. This approach is used by all likelihood-based phylogenetics tools, such as RevBayes [], BEAST [], RAxML [], HyPhy [], PAML [], PHYLIP [], TREE-PUZZLE [], and XRate []. Many more bioinformatics tools use the Dayhoff PAM matrix or other substitution matrix based on an underlying master equation of the form Eq. . […]

library_books

Antibody Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences

2014
Mol Biol Evol
PMCID: 4327158
PMID: 25534034
DOI: 10.1093/molbev/msu340

[…] likelihood gains per site and also was more robust to stochastic errors when inferring the initial frequency distributions from small MSAs.At each iteration step, the EM procedure was performed using XRate () over the set of MSAs and the inferred genealogies. Just like when inferring genealogies, all EM runs were performed assuming the best amino acid model as known at the time of the iteration (s […]

call_split

FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets

2014
BMC Bioinformatics
PMCID: 4287512
PMID: 25344302
DOI: 10.1186/1471-2105-15-341
call_split See protocol

[…] for each alignment Di using maximum likelihood tree construction programs such as PhyML[]. Step 2: Estimate a new exchangeability matrix Q’ using the approach described by Le and Gascuel[] and the XRate software[]. Step 3: Compare Q’ and Q, if they are nearly identical, return Q’ as the optimal model. Otherwise, assign Q ← Q’ and goto Step 1. Step 0: Input a set of multiple alignments D and […]

library_books

Estimating Empirical Codon Hidden Markov Models

2012
Mol Biol Evol
PMCID: 3563974
PMID: 23188590
DOI: 10.1093/molbev/mss266

[…] ecM1a and ecM2a to include an HMM structure among the classes, the new models being called ecHMM1a and ecHMM2a (see supplementary text, Supplementary Material online). The tests were performed using Xrate and generally gave more conservative results than the previous tests performed with PAML. We simulated genes distributing according to an underlying HMM, clustering sites that shared similar se […]

library_books

Developing and Applying Heterogeneous Phylogenetic Models with XRate

2012
PLoS One
PMCID: 3367922
PMID: 22693624
DOI: 10.1371/journal.pone.0036898

[…] As a final example of the possibilities that XRate's new model-specification features enable, we present a new grammar for predicting RNA structures which overlap protein-coding regions. XDecoder is based closely on the RNADecoder grammar first […]

library_books

Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains

2011
BMC Bioinformatics
PMCID: 3329461
PMID: 22142146
DOI: 10.1186/1471-2105-12-465

[…] pectation-maximization (EM) algorithm can be applied to estimate the rate matrix from DNA sequence data observed in the leaves of an evolutionary tree. The EM algorithm is implemented in the software XRate [] and has been applied in [] for estimating empirical codon rate matrices. [] uses the eigenvalue decomposition of the rate matrix to calculate the expected time spent in a state and the expect […]

Citations

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XRate institution(s)
Department of Bioengineering, University of California, Berkeley, CA, USA; European Bioinformatics Institute, Hinxton, UK; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
XRate funding source(s)
Supported, in part, by NIH/NHGRI grant 1R01GM076705- 01, a National Science Foundation Graduate Research Fellowship, in part by the UC Berkeley Graduate Opportunity Fellowship, a Wellcome Trust Prize Studentship, an EMBL predoctoral fellowship and in part by a Wellcome Trust fellowship.

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