QmmRAxML statistics

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Citations per year

Number of citations per year for the bioinformatics software tool QmmRAxML
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Tool usage distribution map

This map represents all the scientific publications referring to QmmRAxML per scientific context
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QmmRAxML specifications

Information


Unique identifier OMICS_34137
Name QmmRAxML
Alternative name Q-matrix mixture Randomized Axelerated Maximum Likelihood
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL https://www.mathstat.dal.ca/~hcwang/QmmRAxML/src/
Maintained Yes

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Maintainers


  • person_outline Andrew Roger
  • person_outline Huai-Chun Wang

Publication for Q-matrix mixture Randomized Axelerated Maximum Likelihood

QmmRAxML citations

 (4)
library_books

Divergence and adaptive evolution of the gibberellin oxidase genes in plants

2015
BMC Evol Biol
PMCID: 4587577
PMID: 26416509
DOI: 10.1186/s12862-015-0490-2

[…] ) (κ = 10). The PP (posterior probability) for the sites under positive selection was calculated by the Bayes empirical Bayes (BEB) method [].Default options were used in the GroupSim and FunDi using QmmRAxML []. In order to evaluate the predictions made by FunDi, we analyzed all the comparisons of eight GAox subfamilies, except for the C19-GAox/C20-GA2ox and C20-GA2ox/GAox-C, due to their large d […]

library_books

Functional Divergence and Convergent Evolution in the Plastid Targeted Glyceraldehyde 3 Phosphate Dehydrogenases of Diverse Eukaryotic Algae

2013
PLoS One
PMCID: 3728087
PMID: 23936198
DOI: 10.1371/journal.pone.0070396

[…] striking, as the homologous position in cytosolic GAPDHs is generally a conserved proline.Residues of interest are also located near to arginine 77 (positions 74, 75, and 76) predicted by FunDi with QmmRAxML as being functionally divergent in both groups of NADPH-dependent GAPDH sequences, along with position 79, which was predicted to be divergent in both groups only by GroupSim. To our knowledg […]

library_books

PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site specific covarion pattern analysis

2009
BMC Evol Biol
PMCID: 2758850
PMID: 19737395
DOI: 10.1186/1471-2148-9-225

[…] hus, for a real example, the covarion model appears to be less susceptible to the effects of LBA than the RAS model. We recently also used a site-specific class frequency mixture model implemented in QmmRAxML [] to analyze the data and found the mixture model supported the correct topology, albeit with a smaller log likelihood gain (Table ). Therefore, in this particular case, the LBA problem can […]

call_split

A class frequency mixture model that adjusts for site specific amino acid frequencies and improves inference of protein phylogeny

2008
BMC Evol Biol
PMCID: 2628903
PMID: 19087270
DOI: 10.1186/1471-2148-8-331
call_split See protocol

[…] class frequency or the whole data set frequency separately. We also account for rates-across-sites using standard discretized gamma mixture model methods. The cF mixture model has been implemented in QmmRAxML, based on the source code of the phylogenetic inference package RAxML.We used QmmRAxML to calculate likelihoods of 25 protein data sets under the single frequency model (JTT + F + Γ) and the […]


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QmmRAxML institution(s)
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics (CGEB), Dalhousie University, Halifax, NS, Canada
QmmRAxML funding source(s)
Supported by a Summer Studentship from the Natural Sciences and Engineering Research Council of Canada (NSERC), Discovery grants awarded, the E.W.R Steacie Memorial Fellowship (NSERC), a research fellowship from the Alfred P. Sloan Foundation and a CGEB postdoctoral fellowship from the Tula Foundation.

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