jModelTest protocols

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jModelTest specifications

Information


Unique identifier OMICS_11546
Name jModelTest
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Database management system MySQL
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.1.10
Stability Stable
High performance computing Yes
Maintained Yes

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Documentation


Maintainer


  • person_outline David Posada <>

Additional information


https://drive.google.com/drive/folders/0ByrkKOPtF_n_OUs3d0dNcnJPYXM

Publications for jModelTest

jModelTest in pipelines

 (299)
2018
PMCID: 5751821
PMID: 29295716
DOI: 10.1186/s13071-017-2577-7

[…] mf693831–mf693833)., bayesian inference (bi) and monte carlo markov chain (mcmc) analysis in mrbayes v.3.2.3 [] were used for phylogenetic analysis. akaike information criteria (aic) test in jmodeltest v.2.1.7 [] was used to evaluate the likelihood parameters set for bi analysis. posterior probability (pp) values were calculated by running 2,000,000 generations with four simultaneous […]

2018
PMCID: 5761093
PMID: 29316927
DOI: 10.1186/s12936-017-2157-5

[…] reconstruction (additional files , ). the best-fit substitution model for the multiple sequence alignment generated by muscle was determined using the bayesian information criteria (bic) strategy in jmodeltest []. evolutionary relationships of the aligned sequences were determined using neighbour-joining (nj) and maximum likelihood (ml) approaches in mega 7.0 [] based on the p-distance method […]

2018
PMCID: 5769553
PMID: 29335015
DOI: 10.1186/s13071-018-2615-0

[…] the bayesian inference method using mrbayes v.3.2.5 [, ]. the best-fit substitution models f81 + g (clock gene) and sym + g (cpr gene) were selected following the bic criterion as implemented in jmodeltest []. indel information was included in the analysis after coding gaps into a binary matrix using fastgap software []. analysis ran for 5,000,000 generations (mcmc - 'burn-in' = 25%) […]

2018
PMCID: 5773594
PMID: 29348650
DOI: 10.1038/s41598-018-19620-7

[…] (72 °c, 10 min). sequences were aligned, proofread and edited in geneious 4.8 (biomatters; http://www.geneious.com). nucleotide substitution models (using 3 substitution schemes) were compared with jmodeltest 2 and best-fit models selected based on the akaike information criterion. bayesian analyses were performed using mrbayes 3. two parallel metropolis-coupled markov chain monte carlo […]

2018
PMCID: 5787326
PMID: 29373979
DOI: 10.1186/s12985-018-0931-9

[…] were built by phyml software [–]. maximum likelihood was used as the criterion to infer phylogenetic relationships between the isolates. the appropriate nucleotide substitution model was selected by jmodeltest program version 2.1.4 []. the visualization and edition of the phylogenetic trees were performed using figtree v.1.4.1., a complete genome of the tospovirus tomato chlorotic spot virus […]


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jModelTest in publications

 (1787)
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] phylogenies of rna polymerase ii and beta tubulin genes were estimated by automatically aligning the nucleotide sequences with mafft [], estimating the custom model of nucleotide substitution with jmodeltest 2.1.10 [] and generating the phylogenetic tree by phyml 3.1 []. the alpha parameter of the gamma distribution of substitution rate categories and the proportion of invariable sites […]

PMCID: 5946424
PMID: 29747566
DOI: 10.1186/s12864-018-4749-z

[…] criteria mentioned above., maximum likelihood (ml) trees were reconstructed from the y-chromosome sequence using raxml (8.1.13) with 1000 bootstrap replicates []. the gtr+ i model was identified by jmodeltest2 as the best fitting substitution model of 12 candidates as determined by the lowest aic []. we estimated the time of the most recent common ancestor (tmrca) for branches of interest using […]

PMCID: 5958175
PMID: 29780270
DOI: 10.3897/mycokeys.25.23836

[…] were aligned separately using muscle () and improved manually using mega v.7 (). the nucleotide substitution model for maximum likelihood (ml) and bayesian inference (bi) analyses was chosen using jmodeltest v.2.1.4 () with the akaike information criterion (aic). the ml tree was performed on the cipres supercomputer using the programme raxml-hpc2 v.8.2.10 on xsede () and bootstrap values […]

PMCID: 5946514
PMID: 29747573
DOI: 10.1186/s12864-018-4762-2

[…] tensis strains were used. the parameters of the evolutionary model were determined by estimating the work of 88 different substitution models on the matrix of the genomes multiple alignment using the jmodeltest2 program [, ]. the following model parameters were defined: priority model gtr + i + g, rateac = 0.972, rateag = 3.369, rateat = 0.496, ratecg = 0.555, rategt = 0.995, proportion invariant  […]

PMCID: 5941070
PMID: 29739906
DOI: 10.1128/mBio.02109-17

[…] by manual editing to discard sequencing and alignment errors. maximum-likelihood (ml) trees were constructed using phyml 3.0 (), with the nucleotide substitution model (gtr+g) inferred by using jmodeltest (). the bootstrap test (1,000 replicates) was used to calculate branch support. only support values of >90% were considered statistically significant. to determine possible […]


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jModelTest institution(s)
Department of Electronics and Systems, University of A Coruña, A Coruña, Spain; Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
jModelTest funding source(s)
Supported by the European Research Council (ERC- 2007-Stg 203161- PHYGENOM), by the Ministry of Science and Innovation of Spain under Projects TIN2010-16735, and by an Amazon Web Services (AWS) research grant ‘‘EC2 in phylogenomics’’.

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