OLDMRBAYESHYBRID_TG
paramfile_ - Results - Input parameters
infile_ - Primary Input File
ALL_FILES_ - Results -
mrbayesblockquery_ - Switch - My Data Contains a MrBayes Data Block (CHECK THIS OR MrBayes BLOCK ENTRIES WILL BE OVERWRITTEN!!!)
set_autoclose_confirm_ - Switch - I confirm that there is not an "autoclose = no" statement in my MrBayes block
nruns_specified_ - Integer - My MrBayes Block specifies nruns=
nchains_specified_ - Integer - My MrBayes Block specifies nchains=
ngen_specified_ - Integer - How many generations will your job run?
sample_freq_ - Integer - What is the sample frequency for your data set?
is_partitioned_ - Switch - My data set is partitioned
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
Section: ****************************************************************************
treeopts
*************************************************************************************
outgroupopts_ - String - Set the Outgroup (enter the name or number of the root taxon)
applyconstraints_ - Switch - Apply constraints to the inferred tree?
constraintoptions_ - Integer - How Many Constraints? (up to 4 may be defined)
taxonidconstraint1_ - String - Enter taxa names or numbers for Constraint1, separated by spaces
taxonidconstraint2_ - String - Enter taxa names or numbers for Constraint2, separated by spaces
taxonidconstraint3_ - String - Enter taxa names or numbers for Constraint3, separated by spaces
taxonidconstraint4_ - String - Enter taxa names or numbers for Constraint1, separated by spaces
Section: ****************************************************************************
lsetopts
*************************************************************************************
nstopts_ - Excl - Set the number of substitution types (Nst=)
nucmodelopts_ - Excl - Set the nucleotide substitution model (Nucmodel=)
codonopts_ - Excl - Set the Codon translation table (Codon=)
omegavaropts_ - Excl - Allow the nonsynonymous/synonymous rate ratio (omega) (Omegavar=)
rateopts_ - Excl - Set the model for among-site rate variation (Rates=)
Ngammacatopts_ - Integer - Set number of rate categories for gamma distribution (Ngammacat=)
Nbetacatopts_ - Integer - Set number of rate categories for beta distribution (Nbetacat=)
Covarionopts_ - Switch - Force the use of covarion-like model (4X4 dna model, or protein) (Covarion=)
codingopts_ - Excl - Specify how characters were sampled (Coding=)
Parsmodelopts_ - Switch - Force calculation under a Parsimony model (Parmodel=)
Section: ****************************************************************************
prsetparams
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tratioopts_ - Excl - Transition/Transversion Ration; DNA only (Tratiopr=)
betameanx_ - Float - Beta mean x
betavary_ - Float - Beta variance y
tratiofixed_ - Float - Fixed Transition/Transversion Ratio
revmatpropts_ - Excl - Substitution Rates of the GTR Model; Nucleic Data only (Revmatpr=)
atocrate_ - Float - A/C rate
atograte_ - Float - A/G rate
atotrate_ - Float - A/T rate
ctograte_ - Float - C/G rate
ctotrate_ - Float - C/T rate
gtotrate_ - Float - G/T Rate
fixedatocrate_ - Float - A/C rate
fixedatograte_ - Float - A/G rate
fixedatotrate_ - Float - A/T rate
fixedctograte_ - Float - C/G rate
fixedctotrate_ - Float - C/T rate
fixedgtotrate_ - Float - G/T Rate
aamodelpropts_ - Excl - Set the Rate Matrix for Amino Acids (Aamodelpr=)
omegapropts_ - Excl - Nonsynonymous/Synonymous Rate Ratio (Omegapr=)
omegaprdir1_ - Float - Uniform Omega Rate1
omegaprdir2_ - Float - Uniform Omega Rate2
omegaprexponential_ - Float - Exponential Omega Rate
omegafixed_ - Float - Fixed Omega Rate
ny98omega1propts_ - Excl - Nonsynonymous/Synonymous Rate Ratio for sites under purifying selection (Ny98omega1pr=)
ny98omega1prbeta1_ - Float - Ny98omega1 Beta Rate 1
ny98omega1prbeta2_ - Float - Ny98omega1 Beta Rate 2
ny98omega1prfix1_ - Float - Fixed Ny98Omega1 Rate
ny98omega3propts_ - Excl - Nonsynonymous/Synonymous Rate Ratio for sites under purifying selection (Ny98omega1pr=)
ny98omega3pruni1_ - Float - Ny98 Uniform Omega Rate 1 for Positive Selection
ny98omega3pruni2_ - Float - Ny98 Uniform Omega Rate 2 for Positive Selection
ny98omega3prexp1_ - Float - Ny98 Exponential Omega Rate for Positive Selection
ny98omega3prfix1_ - Float - Ny98 Fixed Omega Rate for Positive Selection
codoncatfreqsopts_ - Excl - Frequencies of sites under Purifying, Neutral, and Positive Selection (Codoncatfreqs=)
codoncatfreqsdir1_ - Float - Codoncatfreqs Dirichlet Parameter 1
codoncatfreqsdir2_ - Float - Codoncatfreqs Dirichlet Parameter 2
codoncatfreqsdir3_ - Float - Codoncatfreqs Dirichlet Parameter 3
codoncatfreqsfix1_ - Float - Codoncatfreqs Fixed Parameter 1
codoncatfreqsfix2_ - Float - Codoncatfreqs Fixed Parameter 2
codoncatfreqsfix3_ - Float - Codoncatfreqs Fixed Parameter 3
statewfreqpropts_ - Excl - State Frequencies (Statefreqpr=); Assigning frequencies to each state is not supported
statewfreqprdir1_ - Float - Statefreqs Dirichlet Parameter (A single number)
shapepropts_ - Excl - Gamma Shape Parameter (Shapepr=)
shapepruni1_ - Float - Gamma Shape Uniform Parameter 1
shapeprdir2_ - Float - Gamma Shape Dirichlet Parameter 2
shapeprexp1_ - Float - Gamma Shape Exponential Parameter
shapeprfix1_ - Float - Gamma Shape Fixed Parameter
pinvarpropts_ - Excl - Proportion of Invariable Sites (Pinvarpr=)
pinvarpruni1_ - Float - Invariable Sites, Uniform Parameter 1
pinvarpruni2_ - Float - Invariable Sites, Uniform Parameter 2
pinvarprfix1_ - Float - Invariable Sites, Fixed Parameter
ratecorrpropts_ - Excl - Autocorrelation Parameter for Gamma Distribution for Among SIte Variation (Ratecorrpr=)
ratecorrpruni1_ - Float - Autocorrelation Uniform Parameter 1
ratecorrpruni2_ - Float - Autocorrelation Uniform Parameter 2
ratecorrprfix1_ - Float - Autocorrelation Fixed Parameter
covswitchpropts_ - Excl - Covrion Switching Rates (Covswitchpr=)
covswitchuni1_ - Float - Covarion Model Off to On Rate (Uniform)
covswitchuni2_ - Float - Covarion Model On to Off Rate (Uniform)
covswitchexp1_ - Float - Covarion Model Exponential Parameter
covswitchfix1_ - Float - Covarion Model Off to On Rate (Fixed)
covswitchfix2_ - Float - Covarion Model On to Off Rate (Fixed)
symdirihyperpropts_ - Excl - Stationary frequencies for states in standard data sets (Symdirihyperpr=)
symdiruni1_ - Float - Stationary Frequency Uniform Param 1
symdiruni2_ - Float - Stationary Frequency Uniform Param 2
symdirexp1_ - Float - Stationary Frequency Exponential Param 1
symdirfix1_ - Float - Stationary Frequency Fixed Param 1
topologypropts_ - Excl - Specify Topological Constraint Types (Topologypr=)
constraintnames1_ - String - Enter the names or numbers of the constraints to be used, separated by commas
brlenspropts_ - Excl - Probability distribution on branch lengths (Brlenspr=)
brlenspruni2_ - Float - Unconstrained Uniform Param 2
brlensprexp1_ - Float - Unconstrained Exponential Param
treeheightpropts_ - Excl - Distribution on Tree Height (for Clock Models) (Treeheightpr=)
treeheightsprgamma1_ - Float - Gamma Param 1
treeheightsprgamma2_ - Float - Unconstrained Uniform Param 2
treeheightsprexp1_ - Float - Unconstrained Exponential Param
ratepropts_ - Excl - Site Specific Rates Models (Ratespr=)
speciationpropts_ - Excl - Speciation Rate (for Birth:Death Clock Models) (Speciationpr=)
speciationpruni1_ - Float - Speciationpr Uniform Param 1
speciationpruni2_ - Float - Speciationpr Uniform Param 2
speciationprexp1_ - Float - Speciationpr Exponential Param
speciationprfix1_ - Float - Speciationpr Fixed Param
extinctionpropts_ - Excl - Extinction Rate (for Birth:Death Clock Models) (Extinctionpr=)
extinctionpruni1_ - Float - Extinctionpr Uniform Param 1
extinctionpruni2_ - Float - Extinctionpr Uniform Param 2
extinctionprexp1_ - Float - Extinctionpr Exponential Param
extinctionprfix1_ - Float - Extinctionpr Fixed Param
sampleprobopts_ - Float - Fraction of Species Samples in Birth Death Analysis (SampleprobExtinctionpr=)
thetapropts_ - Excl - Prior on the coalescence parameter (nucleic acid data) (Thetapr=)
thetapruni1_ - Float - Thetapr Uniform Param 1
thetapruni2_ - Float - Thetapr Uniform Param 2
thetaprexp1_ - Float - Thetapr Exponential Param
thetaprfix1_ - Float - Thetapr Fixed Param
Section: ****************************************************************************
datamodifications
*************************************************************************************
databreaksopts_ - String - Specify Breaks in Sequence Data (Protein and Nucleic Acid Data only)
pairsopts_ - String - Specify nucleotide pairs involved in Watson-Crick pairing (pairs nucmodel=doublet only)
Section: ****************************************************************************
Charset
*************************************************************************************
nocharsets_ - Excl - How many character sets would you like to define? See the note below.
charset1_ - String - Name for character set 1
charset1range_ - String - Character set 1 range
charset2_ - String - Name for character set 2
charset2range_ - String - Character set 2 range
charset3_ - String - Name for character set 3
charset3range_ - String - Character set 3 range
charset4_ - String - Name for character set 4
charset4range_ - String - Character set 4 range
charset5_ - String - Name for character set 5
charset5range_ - String - Character set 5 range
charset6_ - String - Name for character set 6
charset6range_ - String - Character set 6 range
charset7_ - String - Name for character set 7
charset7range_ - String - Character set 7 range
charset8_ - String - Name for character set 8
charset8range_ - String - Character set 8 range
excludeopts_ - String - Exclude these characters from the analysis
Section: ****************************************************************************
mcmcparams
*************************************************************************************
ngenval_ - Integer - Number of Generations (Ngen=)
seed_ - Integer - Seed=
swapseed_ - Integer - Swapseed=
nrunsval_ - Integer - Number of Runs (nruns=)
nchainsval_ - Integer - Number of Chains to Run (nchains=)
tempval_ - Float - Temperature parameter (temp=)
swapfreqval_ - Integer - How often should swap of states be attempted
nswapsval_ - Integer - How many swaps should be tried per generation
samplefreqval_ - Integer - How often should the Markov chain be sampled?
mcmcdiagnval_ - Excl - Write acceptance ratios of moves and swaps to file?
minpartfreqval_ - Float - Minimum frequency for a partition to be included (minpartfreq)
allchainsval_ - Excl - Record acceptance ratios for all chains?
relburninval_ - Excl - Discard a proportion of the sampled values as burnin when calculating the convergence diagnostic?
burninfracval_ - Float - Specify the fraction of the sampled values discarded as burnin
burninval_ - Integer - Specify the number of sampled values discarded as burnin
stopruleval_ - Excl - Stop early if the convergence diagnostic falls below the stop value?
stopval_ - Float - Stop early if the convergence diagnostic falls below the stop value?
npertsval_ - Integer - Number of random perturbations to apply to user starting tree.
sbrlensval_ - Excl - Save branch length information?
ordertaxaval_ - Excl - Should taxa be ordered before trees are printed to file?
Section: ****************************************************************************
outputopts
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Section: ****************************************************************************
sumtintro
*************************************************************************************
tratioval_ - Excl - Report format for the transition and transversion rates of a nucleotide substitution model with nst=2
revmatopts_ - Excl - Report format for substitution rates of a GTR substitution model for nucleotide or amino acid data
reportancstateopts_ - Switch - Report the probability of ancestral states at all constrained nodes
reportsiterateopts_ - Switch - Report mean site rate in the posterior
reportposselopts_ - Switch - Write Mean Omega Values
Section: ****************************************************************************
sumtintro
*************************************************************************************
sumtburnin_ - Integer - Sumt Burnin Value
sumtnruns_ - Integer - How many .t files should be summarized (Sumt nruns=)
sumtntrees_ - Integer - How many trees should be in the Sumt model
sumtdisplaygeq_ - Float - Minimum probability of partitions to display in Sumt (0.05 = 95%)
sumtcontype_ - Excl - Type of consensus tree
sumtshowtreeprobs_ - Excl - Show Tree Probabilities
Section: ****************************************************************************
sumpintro
*************************************************************************************
sumpburnin_ - Integer - Sump Burnin Value
sumpnruns_ - Integer - How many '.p' files from independent analyses will be summarized (sump Nruns=)
sumpplot_ - Excl - Prepare a likelihood plot
sumpmarglike_ - Excl - Calculate estimates of marginal model likelihoods
sumptable_ - Excl - Prepare a table summarizing the parameter value samples