jModelTest specifications

Information


Unique identifier OMICS_11546
Interface Web user interface
Restrictions to use None
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_11546
Software type Package/Module
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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jModelTest articles

jModelTest citations

 (72)
2018
PMCID: 5924500

[…] based on the sequence data, the most suitable likelihood parameters and evolutionary models were determined using the akaike information criteria test in the program jmodeltest version 3.7 [26]. jmodeltest revealed that the most suitable model for the its1, its2 and its+ were tpm1uf+i, tpm3uf and gtr+i+g, respectively. the bi analysis was conducted, employing the markov chain monte carlo […]

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: 5851586

[…] retrieved from genbank (table 1). all sequences were aligned with muscle [47] in mega 6 [48]., * sequences obtained in the present study, the best nucleotide substitution model was selected with jmodeltest [49]. phylogenetic analyses were carried out with concatenated sequences of genes rag1, coi and 16s for the hosts and coi and partial its region, (5.8s + its2) for the parasites. […]

2018
PMCID: 5790234

[…] present being considered as 2017), the isolation years of the modern strains, and a substitution rate of 6.87 × 10−9 substitutions per site per year as estimated by [19] were used as priors. using jmodeltest2 [48], the kimura 3-parameter model with unequal base frequencies was determined to be the best model of nucleotide substitution. a strict clock model with uniform rate across branches […]

2017
PMCID: 5704249

[…] among the genus bifidobacterium were constructed using groel gene. the best fitted substitution model for each partition was estimated using akaike information criterion (aic) implemented in jmodeltest [29]. the model of tim1 + i + g was chosen for maximum likelihood (ml) analyses, which were performed with raxml blackbox web servers [30]., all available bifidobacterial […]

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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