MrBayes REST


MrBayes REST interface:

This interface can be used from the REST API in two ways. The easiest way is to require the user to provide an input file with a MrBayes block to configure the run. An auxiliary file called paramfile.txt will also be created to provide some additional parameters, even if a MrBayes block is used. Alternatively, the interface supports setting of most MrBayes options, which are then added to the file paramfile.txt, and submitted to set the configuration. Uploading a starting tree via the interface is not supported, however. You must use a MrBayes block for this. MrBayes reads the MrBayes block of the input file first, and then paramfile.txt. So if a user submits an input data file with a MrBayes block, and a paramfile.txt, the latter values will be respected, as the MrBayes block values will be overwritten. To try to prevent this, interface options that write to the paramfile.txt file are disabled when the user acknowledges that MrBayes block is present.

The Tool ID for this interface is MRBAYES_XSEDE. It is selected with toolId=MRBAYES_XSEDE

Supported uploaded files:
input.infile_ - Primary Input File

Supported parameters are:
For all runs.
vparam.runtime_ - Float - Maximum Hours to Run. Max = 168, default=0.25.
vparam.set_beagle_params_ - Switch - Run BEAGLE (default=1, beagle is used.)

For an input file with a MrBayes block, supported parameters are:
vparam.mrbayesblockquery_ - Switch - Specifies a MB block is used when set to 1. My Data Contains a MrBayes Data Block. (default=0)
vparam.nruns_specified_ - Integer - My MrBayes Block specifies nruns= (required when mrbayesblockquery_=1.)(default=2) Helps set run configuration.
vparam.nchains_specified_ - Integer - My MrBayes Block specifies nchains= (required when mrbayesblockquery_=1.) (default=4) Helps set run configuration.

For an input file with NO MrBayes block, supported parameters are:
(these will be added to the file paramfile.txt, which is created by the interface, and submitted with other input to the working directory)
vparam.flagdatatype_ - Excl - My Data Type Is (only one data type can be used with no MB block) allowed: dna, protein, standard, other, default=dna
vparam.seed_ - Integer - Set the Seed Number Set seed= (not required, no default)
vparam.swapseed_ - Integer - Set the Swapseed= (not required, no default)
vparam.scientific_ - Switch - Use scientific notation (not required, default=0)
vparam.precision_ - Integer - How many decimals should we print? integer between 3 and 15, (not required, default=15)
vparam.set_outgroup_ - String - Specify (only) one outgroup (no default, not required).

****************************************************************************
likelihood settting (lset) options; defaults and value options as in MrBayes command reference
****************************************************************************
vparam.nstopts_ - Excl - Set the number of substitution types (Nst=)
vparam.nucmodelopts_ - Excl - Set the nucleotide substitution model (Nucmodel=)
vparam.codonopts_ - Excl - Set the Codon translation table (Codon=)
vparam.omegavaropts_ - Excl - Allow the nonsynonymous/synonymous rate ratio (omega) (Omegavar=)
vparam.ploidyopts_ - Excl - Set the ploidy (Ploidy=)
vparam.rateopts_ - Excl - Set the model for among-site rate variation (Rates=)
vparam.Ngammacatopts_ - Integer - Set number of rate categories for gamma distribution (Ngammacat=)
vparam.Nbetacatopts_ - Integer - Set number of rate categories for beta distribution (Nbetacat=)
vparam.Covarionopts_ - Switch - Force the use of covarion-like model (4X4 dna model, or protein) (Covarion=)
vparam.codingopts_ - Excl - Specify how characters were sampled (Coding=)
vparam.Parsmodelopts_ - Switch - Force calculation under a Parsimony model (Parmodel=)
*************************************************************************************
prior parameters (prset); defaults and value options as in MrBayes command reference
*************************************************************************************
vparam.tratioopts_ - Excl - Transition/Transversion Rate Ratio; DNA only (Tratiopr=)
vparam.betameanx_ - Float - Beta mean x
vparam.betavary_ - Float - Beta variance y
vparam.tratiofixed_ - Float - Fixed Transition/Transversion Ratio
vparam.revmatpropts_ - Excl - Substitution Rates of the GTR Model; Nucleic Data only (Revmatpr=)
vparam.atocrate_ - Float - A/C rate
vparam.atograte_ - Float - A/G rate
vparam.atotrate_ - Float - A/T rate
vparam.ctograte_ - Float - C/G rate
vparam.ctotrate_ - Float - C/T rate
vparam.gtotrate_ - Float - G/T Rate
vparam.fixedatocrate_ - Float - A/C rate
vparam.fixedatograte_ - Float - A/G rate
vparam.fixedatotrate_ - Float - A/T rate
vparam.fixedctograte_ - Float - C/G rate
vparam.fixedctotrate_ - Float - C/T rate
vparam.fixedgtotrate_ - Float - G/T Rate
vparam.aamodelpropts_ - Excl - Set the Rate Matrix for Amino Acids (Aamodelpr=)
vparam.omegapropts_ - Excl - Nonsynonymous/Synonymous Rate Ratio (Omegapr=)
vparam.omegaprdir1_ - Float - Uniform Omega Rate1
vparam.omegaprdir2_ - Float - Uniform Omega Rate2
vparam.omegaprexponential_ - Float - Exponential Omega Rate
vparam.omegafixed_ - Float - Fixed Omega Rate
vparam.ny98omega1propts_ - Excl - Nonsynonymous/Synonymous Rate Ratio for sites under purifying selection (Ny98omega1pr=)
vparam.ny98omega1prbeta1_ - Float - Ny98omega1 Beta Rate 1
vparam.ny98omega1prbeta2_ - Float - Ny98omega1 Beta Rate 2
vparam.ny98omega1prfix1_ - Float - Fixed Ny98Omega1 Rate
vparam.ny98omega3propts_ - Excl - Nonsynonymous/Synonymous Rate Ratio for sites under positive selection (Ny98omega3pr=)
vparam.ny98omega3pruni1_ - Float - Ny98 Uniform Omega Rate 1 for Positive Selection
vparam.ny98omega3pruni2_ - Float - Ny98 Uniform Omega Rate 2 for Positive Selection
vparam.ny98omega3prexp1_ - Float - Ny98 Exponential Omega Rate for Positive Selection
vparam.ny98omega3prfix1_ - Float - Ny98 Fixed Omega Rate for Positive Selection
vparam.M3omega3propts_ - Excl - Nonsynonymous/Synonymous Rate Ratio for sites under the M3 model (M3omega1pr=)
vparam.M3omega3prfix1_ - Float - M3 Fixed Omega Rate 1 for M3 Model
vparam.M3omega3prfix2_ - Float - M3 Fixed Omega Rate 2 for M3 Model
vparam.M3omega3prfix3_ - Float - M3 Fixed Omega Rate 3 for M3 Model
vparam.codoncatfreqsopts_ - Excl - Frequencies of sites under Purifying, Neutral, and Positive Selection (Codoncatfreqs=)
vparam.codoncatfreqsdir1_ - Float - Codoncatfreqs Dirichlet Parameter 1
vparam.codoncatfreqsdir2_ - Float - Codoncatfreqs Dirichlet Parameter 2
vparam.codoncatfreqsdir3_ - Float - Codoncatfreqs Dirichlet Parameter 3
vparam.codoncatfreqsfix1_ - Float - Codoncatfreqs Fixed Parameter 1
vparam.codoncatfreqsfix2_ - Float - Codoncatfreqs Fixed Parameter 2
vparam.codoncatfreqsfix3_ - Float - Codoncatfreqs Fixed Parameter 3
vparam.statewfreqpropts_ - Excl - State Frequencies (Statefreqpr=); Assigning frequencies to each state is not supported
vparam.statewfreqprdir1_ - Float - Statefreqs Dirichlet Parameter (A single number)
vparam.shapepropts_ - Excl - Gamma Shape Parameter (Shapepr=)
vparam.shapepruni1_ - Float - Gamma Shape Uniform Parameter 1
vparam.shapeprdir2_ - Float - Gamma Shape Dirichlet Parameter 2
vparam.shapeprexp1_ - Float - Gamma Shape Exponential Parameter
vparam.shapeprfix1_ - Float - Gamma Shape Fixed Parameter
vparam.pinvarpropts_ - Excl - Proportion of Invariable Sites (Pinvarpr=)
vparam.pinvarpruni1_ - Float - Invariable Sites, Uniform Parameter 1
vparam.pinvarpruni2_ - Float - Invariable Sites, Uniform Parameter 2
vparam.pinvarprfix1_ - Float - Invariable Sites, Fixed Parameter
vparam.ratecorrpropts_ - Excl - Autocorrelation Parameter for Gamma Distribution for Among SIte Variation (Ratecorrpr=)
vparam.ratecorrpruni1_ - Float - Autocorrelation Uniform Parameter 1
vparam.ratecorrpruni2_ - Float - Autocorrelation Uniform Parameter 2
vparam.ratecorrprfix1_ - Float - Autocorrelation Fixed Parameter
vparam.covswitchpropts_ - Excl - Covrion Switching Rates (Covswitchpr=)
vparam.covswitchuni1_ - Float - Covarion Model Off to On Rate (Uniform)
vparam.covswitchuni2_ - Float - Covarion Model On to Off Rate (Uniform)
vparam.covswitchexp1_ - Float - Covarion Model Exponential Parameter
vparam.covswitchfix1_ - Float - Covarion Model Off to On Rate (Fixed)
vparam.covswitchfix2_ - Float - Covarion Model On to Off Rate (Fixed)
vparam.symdirihyperpropts_ - Excl - Stationary frequencies for states in standard data sets (Symdirihyperpr=)
vparam.symdiruni1_ - Float - Stationary Frequency Uniform Param 1
vparam.symdiruni2_ - Float - Stationary Frequency Uniform Param 2
vparam.symdirexp1_ - Float - Stationary Frequency Exponential Param 1
vparam.symdirfix1_ - Float - Stationary Frequency Fixed Param 1
vparam.topologypropts_ - Excl - Specify Topological Constraint Types (Topologypr=)
vparam.constraintnames1_ - String - Enter the names or numbers of the constraints to be used, separated by commas
vparam.brlenspropts_ - Excl - Probability distribution on branch lengths (Brlenspr=)
vparam.brlenspruni2_ - Float - Unconstrained Uniform Param 2
vparam.brlensprexp1_ - Float - Unconstrained Exponential Param
vparam.treeheightpropts_ - Excl - Distribution on Tree Height (for Clock Models) (Treeagepr=)
vparam.treeheightsprgamma1_ - Float - Gamma Param 1
vparam.treeheightsprgamma2_ - Float - Unconstrained Uniform Param 2
vparam.treeheightsprexp1_ - Float - Unconstrained Exponential Param
vparam.treeheightsprfx1_ - Float - Treeagepr Fixed Param
vparam.ratepropts_ - Excl - Site Specific Rates Models (Ratepr=)
vparam.speciationpropts_ - Excl - Speciation Rate (for Birth:Death Clock Models) (Speciationpr=)
vparam.speciationpruni1_ - Float - Speciationpr Uniform Param 1
vparam.speciationpruni2_ - Float - Speciationpr Uniform Param 2
vparam.speciationprexp1_ - Float - Speciationpr Exponential Param
vparam.speciationprfix1_ - Float - Speciationpr Fixed Param
vparam.extinctionpropts_ - Excl - Extinction Rate (for Birth:Death Clock Models) (Extinctionpr=)
vparam.extinctionpruni1_ - Float - Extinctionpr Beta Param 1
vparam.extinctionpruni2_ - Float - Extinctionpr Beta Param 2
vparam.extinctionprfix1_ - Float - Extinctionpr Fixed Param
vparam.sampleprobopts_ - Float - Fraction of Species Samples in Birth Death Analysis (SampleprobExtinctionpr=)
vparam.thetapropts_ - Excl - Prior on the coalescence parameter (nucleic acid data) (Thetapr=)
vparam.thetapruni1_ - Float - Thetapr Uniform Param 1
vparam.thetapruni2_ - Float - Thetapr Uniform Param 2
vparam.thetaprexp1_ - Float - Thetapr Exponential Param
vparam.thetaprfix1_ - Float - Thetapr Fixed Param
********* ****************************************************************************
data modifications: defaults and value options as in MrBayes command reference
*************************************************************************************
vparam.databreaksopts_ - String - Specify Breaks in Sequence Data (Protein and Nucleic Acid Data only)
vparam.pairsopts_ - String - Specify nucleotide pairs involved in Watson-Crick pairing (pairs nucmodel=doublet only)

**************************************************************************************
charset options: Use this to define character sets; all defaults and values as in MrBayes command reference.:
*************************************************************************************
vparam.nocharsets_ - Excl - How many character sets would you like to define? (allowed values: 1-8) This activates the
correct number of charsetX_ options below.
vparam.charset1_ - String - Name for character set 1
vparam.charset1range_ - String - Character set 1 range; adds charset $charset1 = $value to paramfile.txt
vparam.charset2_ - String - Name for character set 2
vparam.charset2range_ - String - Character set 2 range
vparam.charset3_ - String - Name for character set 3
vparam.charset3range_ - String - Character set 3 range
vparam.charset4_ - String - Name for character set 4
vparam.charset4range_ - String - Character set 4 range
vparam.charset5_ - String - Name for character set 5
vparam.charset5range_ - String - Character set 5 range
vparam.charset6_ - String - Name for character set 6
vparam.charset6range_ - String - Character set 6 range
vparam.charset7_ - String - Name for character set 7
vparam.charset7range_ - String - Character set 7 range
vparam.charset8_ - String - Name for character set 8
vparam.charset8range_ - String - Character set 8 range
vparam.excludeopts_ - String - Exclude these characters from the analysis, using the"exclude $value" command
*************************************************************************************
mcmc parameters - defaults and value options as in MrBayes command reference
*************************************************************************************
vparam.ngenval_ - Integer - Number of Generations (Ngen=)
vparam.nrunsval_ - Integer - Number of Runs (nruns=)
vparam.nchainsval_ - Integer - Number of Chains to Run (nchains=)
vparam.tempval_ - Float - Temperature parameter (temp=)
vparam.swapfreqval_ - Integer - How often should swap of states be attempted (swapsfreq=)
vparam.nswapsval_ - Integer - How many swaps should be tried per generation (nswaps=)
vparam.samplefreqval_ - Integer - How often should the Markov chain be sampled? (samplefreq=)
vparam.specify_diagnfreqval_ - Integer - Number of generations between the calculation of MCMC diagnostics (default=5000)
vparam.mcmcdiagnval_ - Excl - Write acceptance ratios of moves and swaps to file? (mcmcdiagn=Yes/No)
vparam.minpartfreqval_ - Float - Minimum frequency for a partition to be included (minpartfreq=)
vparam.allchainsval_ - Excl - Record acceptance ratios for all chains? (allchains=)
vparam.relburninval_ - Excl - Discard a proportion of the sampled values as burnin when calculating the convergence diagnostic? (relburnin=)
vparam.burninfracval_ - Float - Specify the fraction of the sampled values discarded as burnin (burninfrac=)
vparam.burninval_ - Integer - Specify the number of sampled values discarded as burnin (burnin=), burnin and burninfrac are mutually exclusive
vparam.stopruleval_ - Excl - Stop early if the convergence diagnostic falls below the stop value? (stoprule=)
vparam.stopval_ - Float - Stop early if the convergence diagnostic falls below the stop value? (stop=)
vparam.npertsval_ - Integer - Number of random perturbations to apply to user starting tree. (nperts=)
vparam.sbrlensval_ - Excl - Save branch length information? (Savebrlens=Yes/No)
vparam.ordertaxaval_ - Excl - Should taxa be ordered before trees are printed to file? (Ordertaxa=Yes/No)

***********************************************************************************
sumt parameters; defaults and value options as in MrBayes command reference
*************************************************************************************
vparam.tratioval_ - Excl - Report format for the transition and transversion rates of a nucleotide substitution model with nst=2. (tratio=)
vparam.revmatopts_ - Excl - Report format for substitution rates of a GTR substitution model for nucleotide or amino acid data (report revmat=ratio/dirichelet)
vparam.reportancstateopts_ - Switch - Report the probability of ancestral states at all constrained nodes
vparam.reportsiterateopts_ - Switch - Report mean site rate in the posterior
vparam.reportposselopts_ - Switch - Write Mean Omega Values
*************************************************************************************
sumt parameters; defaults and value options as in MrBayes command reference
*************************************************************************************
vparam.sumtburnin_ - Integer - Sumt Burnin Value
vparam.sumt_relburnin_ - Excl - Discard a specified proportion of samples instead of a specific number(Relburnin=Yes)
vparam.sumt_burninfrac_ - Float - Specify the fraction of samples to be discarded (Burninfrac=)
vparam.sumtnruns_ - Integer - How many .t files should be summarized (Sumt nruns=)
vparam.sumtntrees_ - Integer - How many trees should be in the Sumt model
vparam.sumtdisplaygeq_ - Float - Minimum probability of partitions to display in Sumt (0.05 = 95%)
vparam.sumtcontype_ - Excl - Type of consensus tree
vparam.sumt_conformat_ - Excl - Choose the output format for your consensus tree (Conformat=)
vparam.sumtshowtreeprobs_ - Excl - Show Tree Probabilities

*************************************************************************************
sumpintro; defaults and value options as in MrBayes command reference
*************************************************************************************
vparam.sumpburnin_ - Integer - Sump Burnin Value
vparam.sump_relburnin_ - Excl - Discard a specified proportion of samples instead of a specific number(Relburnin=Yes)
vparam.sump_burninfrac_ - Float - Specify the fraction of samples to be discarded (Burninfrac=)
vparam.sumpnruns_ - Integer - How many '.p' files from independent analyses will be summarized (sump Nruns=)

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