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MrModelTest specifications

Information


Unique identifier OMICS_33377
Name MrModelTest
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 2.4
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Johan Nylander

MrModelTest citations

 (804)
call_split

Characterization of Plasmodium relictum, a cosmopolitan agent of avian malaria

2018
Malar J
PMCID: 5930738
PMID: 29720195
DOI: 10.1186/s12936-018-2325-2
call_split See protocol

[…] he phylogenetic trees (Fig. ). Bayesian phylogenetic tree (Fig. a) was constructed using MrBayes version 3.1 [] software. The General Time Reversible Model (GTR) was used as suggested by the software MrModeltest 2.2 (https://github.com/nylander/MrModeltest2). Analysis was run for a total of 10 million generations with a sampling frequency of every 100 generations. Before the construction of the co […]

call_split

Two new species and one new record of the genus Tylopilus (Boletaceae) from Indian Himalaya with morphological details and phylogenetic estimations

2018
PMCID: 5911683
PMID: 29686503
DOI: 10.3897/mycokeys.33.23703
call_split See protocol

[…] rITS sequences were also phylogenetically analysed using Bayesian analysis. The best-fit models of nucleotide evolution for nrLSU and nrITS datasets (TIMef and TrNef+G, respectively) were obtained in MrModeltest 3.7 (). Bayesian inferences were computed independently twice in MrBayes v.3.2.2 (), under TIMef (for nrLSU) and TrNef+G (for nrITS) models, respectively. Bayesian posterior probabilities […]

library_books

Disjunct distribution and distinct intraspecific diversification of Eothenomys melanogaster in South China

2018
BMC Evol Biol
PMCID: 5894153
PMID: 29636000
DOI: 10.1186/s12862-018-1168-3

[…] nes using Bayesian inference (BI) methods in MrBayes 3.2.5 [] and maximum likelihood (ML) methods in RAxML v.8.2.10 []. The best fit model of nucleotide substitution for each locus was selected using MrModeltest v2.3 []. Two parallel runs of one cold and three heated Markov chain Monte Carlo (MCMC) analyses were performed for 15 million generations or more, with trees sampled every 1,000 generatio […]

call_split

Conserved community structure and simultaneous divergence events in the fig wasps associated with Ficus benjamina in Australia and China

2018
BMC Ecol
PMCID: 5883542
PMID: 29615023
DOI: 10.1186/s12898-018-0167-y
call_split See protocol

[…] eye. Bayesian methods were employed to construct phylogenies for each marker using MrBayes []. The best model of nucleotide substitution for each gene was determined using likelihood ratio tests with MrModeltest in PAUP* []. For both markers the general time reversible (GTR + I + R) model of evolution was chosen.Species richness was calculated using the barcoding criteria of monophyletic lineages […]

library_books

Molecular and morphological data of the freshwater fish Glandulocauda melanopleura (Characiformes: Characidae) provide evidences of river captures and local differentiation in the Brazilian Atlantic Forest

2018
PLoS One
PMCID: 5868800
PMID: 29579069
DOI: 10.1371/journal.pone.0194247

[…] lognormal distribution []; a starting tree was obtained from RAxML analysis; a macroevolutionary Birth–Death model for the diversification likelihood values; and under GTR+I+G model (as estimated in MrModeltest). We included two calibration points based on fossil records of the characids †Paleotetra (Eocene-Miocene, []) and †Megacheirodon unicus (Late Oligocene-Early Miocene, [–]). According to M […]

library_books

Photobiont switching causes changes in the reproduction strategy and phenotypic dimorphism in the Arthoniomycetes

2018
Sci Rep
PMCID: 5862901
PMID: 29563606
DOI: 10.1038/s41598-018-23219-3

[…] rkov chain Monte Carlo (MCMCMC) method in MrBayes v. 3.2.6 on the CIPRES Web Portal. GTR + I + G best-fit evolutionary model was selected based on Akaike Information Criterion (AIC) as implemented in MrModelTest2. Two parallel MCMCMC runs were performed, each using four independent chains and 20 million generations, sampling trees every 1000th. Tracer v. 1.6 was used to ensure that stationarity wa […]

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