jModelTest pipeline

jModelTest specifications

Information


Unique identifier OMICS_11546
Name jModelTest
Software type Application/Script
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 Medium
Version 2.1.10
Stability Stable
High performance computing Yes
Maintained Yes

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Publications for jModelTest

jModelTest citations

 (48)
2018
PMCID: 5829258

[…] and the protein coding fragments were checked for reading frames. the concatenated matrices were analysed under the likelihood criterion using raxml 7.2.361,62 with the model identified by jmodeltest 263 using the aic criterion. the dataset was partitioned by genes and codon positions (table s5) and analysed with 1,000 bootstrap replicates under the gtrcat substitution model61. […]

2018
PMCID: 5905893

[…] eliminated 37% of the mafft alignment, resulting in 121,016 characters and 10,847 distinct alignment patterns in the final alignment (see supplementary material s2 file). both, aic and bic from jmodeltest indicated the general time reversible model using gamma and invariant sites (gtr+i+g) as the best fit. final ml optimization likelihood was -254343.104231. the maximum parsimony analysis […]

2018
PMCID: 5916226

[…] non-coding (the two partial ribosomal rna genes, and eight partial trna genes), mtdna cr, and protein-coding regions. we inferred the best-fitting model for nucleotide evolution under the aic using jmodeltest v.2.1.4 software (darriba et al., 2012). the model of substitution used was tpm1uf+i, tpm3uf+i+g, and tvm+i+g for non-coding partitions, mtdna cr, and protein coding regions, […]

2017
PMCID: 5224923

[…] (nod1_1h-udg) library with muscle v3.8 (edgar, 2004) (rrid:scr_011812). it was determined that the best model of nucleotide substitute for this group of 138 sequences was hky+i+γ using the program jmodeltest2 (darriba et al., 2012) and the built-in akaike information criterion (akaike, 1974). a bayesian maximum clade credibility tree was calculated using beast v1.8 (drummond et al., 2012) […]

2017
PMCID: 5242430

[…] of c. neoformans var. grubii vni isolates were performed as follows: first, the best model for the concatenated dataset was chosen from the bayesian information criterion (bic) using the software jmodeltest 2.1.7 [46, 47]. the tamura nei model with invariable sites and gamma distribution (trnef + i + g) with p-inv: 0.955 and alpha shape: 0.832 was selected and used in the phylogenetic […]

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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