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jModelTest specifications


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




No version available



  • person_outline David Posada

Additional information

Publications for jModelTest

jModelTest citations


Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

BMC Genomics
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 were est […]


Analysis of the canid Y chromosome phylogeny using short read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

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

[…] 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 […]


Architrypethelium murisporum (Ascomycota, Trypetheliaceae), a remarkable new lichen species from Thailand challenging ascospore septation as an indicator of phylogenetic relationships

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

[…] U) 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 were e […]


Global evolution and phylogeography of Brucella melitensis strains

BMC Genomics
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  […]


Re visiting the evolution, dispersal and epidemiology of Zika virus in Asia

PMCID: 5940881
PMID: 29739925
DOI: 10.1038/s41426-018-0082-5
call_split See protocol

[…] uent analyses were performed with a generalized time-reversible nucleotide substitution model with four gamma distributed rate variation categories and a proportion of invariant sites, as selected by jModeltest v.2.To analyze the phylogenies of the 84 Asian lineage strains, including the novel Indian sequence, a Bayesian phylogenetic tree was computed using MrBayes v.3.2.6 with the dataset includi […]


Ceftazidime Is the Key Diversification and Selection Driver of VIM Type Carbapenemases

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

[…] July 2017). The programs used to perform the phylogenetic analysis were the following: (MEGA), (PhyML), (jModeltest), (RDP), (BEAST/Tracer/FigTree), (MESQUITE), and http://www.fluxus-engineerin […]

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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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