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Start Your TrialModelTest-NG determines the best-fit model of evolution for DNA and protein alignments. ModelTest-NG integrates five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It can be used to operate statistical selection of best-fit models of nucleotide substitution or amino acid replacement.
The code runs on 24 cores, and supercedes jModelTest2 and Prottest.
INPUT = dna or protein matrices in aligned fasta format
The Tool ID for this interface is MODELTEST_NG_XSEDE_
Supported uploaded files:done -t -*topology topology type. Check section 5.3
input.infile_ = primary input file, in fas format.
user_fixedtree_ = User-defined fixed tree for likelihood calculations (-u)
user_partitionfile_ = User-defined partition file (-q)
Supported parameters are:
For all runs.
vparam.runtime_ - Float - Maximum Hours to Run. Max = 168, default=0.25.
vparam.specify_datatype_ - Switch - The dataset contains amino acid (-d aa). Default = 0
vparam.asc_bias_ - Excl - Ascertainment bias algorithm (-a) when $set_heterogeneity eq "u"; lewis, felsenstein, stamatakis. felsenstein and stamatakis require number of invariant sites and invariant sites composition (respectively) supplied via partition file.
vparam.name_output_ - String - Specify the name of the output file (-o)
vparam.specify_topology_ - Excl - Specify topology type (-t); ml; mp; fixed-ml-jc; fixed-ml-gtr; random; user
vparam.set_heterogeneity_ - Excl - Select the candidate model's rate heterogeneity (-h); u; i; g; f; Both +I and +G (+I+G)
vparam.specify_seed_ - Integer - Specify a seed value (-r)
DNA Candidate models (specify_datatype=0)
vparam.specify_frequencies_ - Excl - Select the candidate models frequencies (-f):e, f
vparam.model_lists - List - Select the DNA candidate model(s) matrices (-m): JC, HKY, TrN,TPM1,TPM2,TPM3,TIM1, TIM2,TIM3, TVM, GTR, submit each choice separately with a new command.
vparam.set_subschemes_ - Excl - Set the number of substitution schemes (-s): 3,5,7,11, 203
vparam.template_tool_ - Excl - Set DNA candidate models according to a specified tool: raxml, phyml, mrbayes, paup
vparam.model_lists, vparam.set_subschemes, and vparam.template_tool are mutually exclusive.
Protein Candidate Models (specify_datatype =1)
vparam.specify_protfrequencies_ - Excl - Select the candidate protein models frequencies (-f): e, f.
vparam.protmodel_lists_ - List - Enter the Amino Acid candidate model matrices (-m); DAYHOFF,LG,DCMUT,JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, STMTRE.
vparam.set_protsubschemes_ - Excl - Set the number of protein substitution schemes (-s): 3,5,7,11,203 default = 11
protemplate_tool_ - Excl - raxml, phyml, mrbayes, paup
Other options
vparam.set_epsilon_ - Float - Sets the model optimization epsilon. (-eps)
vparam.set_tolerance - Set the parameter optimization tolerance (--tol)
vparam.criteria_1 - Switch - Force frequencies smoothing (--smooth-frequencies)
vparam.disable_patterncompression_ - Swtich - Disables pattern compression (-H)
If you use ModelTest-NG, please cite the Git Repo
If there is a tool or a feature you need, please let us know>