jModeltest2 REST

jModelTest2 interface:

jModelTest2 is used to carry out statistical selection of best-fit models of nucleotide substitution. It implements 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 also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model-averaged phylogenetic trees (both topology and branch length), heuristic filtering and automatic logging of user activity. jModelTest2 on XSEDE submits jobs to Expanse, a large NSF XSEDE Resource. Each job is assigned to 8 cores, which can speed up the results signficiantly relative to the serial version.

The Tool ID for this interface is JMODELTEST2_XSEDE. It is selected with tool=JMODELTEST2_XSEDE
The interface was changed recently, and affected parameters are show in red below.

Supported parameters:

input.infile_ - Primary Input File
input.user_fixedtree_ - infile - Select a User-defined fixed tree for likelihood calculations (-u)

vparam.runtime_ - Float - Maximum Hours to Run (up to 168 hours)
vparam.name_output_ - String - Specify the name of your output file (-o)
vparam.name_suffix_ - String - Specify a suffix for your log file (-n)
vparam.convert_phylip_ - Switch - Convert input to Phylip format (then exit) default=0
vparam.information_criterion_ - Excl - Clustering search (-H); AIC; AICc; BIC (default)
vparam.threshold_heuristic_ - Float - Perform threshold heuristic search. (-G; default = 0.1)
vparam.set_subschemes_ - Excl - Set the number of substitution schemes (-s) default=11, options: 3,5,7,11.203
vparam.uneq_basefmodels_ - Switch - Include models with unequal base frequencies. (-f); default=1
vparam.uneq_basefmodels_ - Excl - Include models with unequal base frequencies. (-f) 1=no 2=yes; default=1
vparam.convert_phylip_ - Switch - Convert input to Phylip format (then exit) default=0
vparam.information_criterion_ - Switch - Specify a seed for this run (by default a random seed is used)
vparam.invar_models_ - Switch - Include models with a proportion invariable sites. (-i) default=1
vparam.invar_models_ - Excl - Include models with a proportion invariable sites. (-i)  1-no, 2=yes, default=2
vparam.numratecat_models_ - Integer - Include models with rate variation among sites, set number of categories (-g; default = 4)
vparam.confidenceint_models_ - Integer - Confidence interval for the model selection process (-c; default = 100)
vparam.set_basetree_ - Excl - Base tree topology for likelihood calculations. (-t): fixed; BIONJ; ML; default=ML
vparam.def_topsearch_ - Excl - Set tree topology search operation option for Maximum-Likelihood search (-S) NNI, SPR, BEST (default)
vparam.criteria_1_ - List - Select Information Criterion (choose all needed) multi selections; -AIC, -AICc,-BIC, -DT
vparam.confidence_selection_ - Float - Confidence level for the hLRTs (-h; default is 0.01)
vparam.parameter_importances_ - Switch - Calculate the parameter importances (-p) default=1
vparam.modeland_importances_ - Switch - Do model averaging and parameter importances (-v) default=0
vparam.print_paup_ - Switch - Print out the PAUP block (-w) default=1
vparam.estimate_modelavg_ - Switch - Estimate model-averaged phylogeny for each active criterion (-a) default=1
vparam.strict_consensus_ - Switch - Use strict consensus type for model-averaged phylogeny (-z) default=0
vparam.calculate_delta_ - Switch - Calculate delta AIC,AICc,BIC against unconstrained likelihood. (-uLnL) default=0
vparam.hierarchical_likelihood_ - Switch - Perform hierarchical likelihood ratio tests (-hLRT) default=0
vparam.specify_hyporder_ - String - Specify the hypothesis order (-O; default ftvwxgp) default=ftvwxgp
vparam.backward_selection_ - Switch - Backward selection for the hLRT (-r) default=0
vparam.dynamical_likelhood_ - Switch - Perform dynamical likelihood ratio tests. (-dLRT) default=0

hummingbird in flight

Get 1000 Hours free

On the UCSD Supercomputer

Start Your Trial