MPboot REST

MPBOOT REST interface:

This interface is used from the REST API to convey input files, and configure the command line MPBOOT parameters.
Note that to our knowledge there is only a serial version of MPBOOT at this time. All runs will be completed on a single processor core.

If you are aware of a multi-core option, please let us know.

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

Supported parameters: Input files:
input.infile_ - Primary Input File
input.initialTree_ - InFile - Specify an initial tree (Newick format)
input.costFile_ InFile - Matrix of transition cost between character states (-cost)
input .consensusTrees_ - InFile - Set of input trees for consensus reconstruction
input.assignSupportvals_ - InFile - Assign support values for this file to .suptree (-sup)
input.rfTreefile_ - InFile - Specify a tree set for RF distances
input.rfdistTwosets_ - InFile - Compute all RF distances between two sets of trees (-rf treefile2)

Supported parameters:
varam.runtime_ - Float - Maximum Hours to Run (0.5=default; 168 = maximum)
vparam.datatype_ - Excl - Input type; default=Auto (DNA, AA,, CODON, MORPH, BIN) Leave blnk for Auto.
vparam.specifyPrefix_ - String - Provide a prefix for output files (-pre) (default=mpboot)
vparam.seed_val_ - Integer - Enter the seed value here. (default = 12345)
vparam.specifyVerbose_ - Switch - Provide verbose output (-vvv) (default=0).
vparam.more_memory_ - Switch - My run ran out of memory; I need more (default=0).

Maximum Parsimony Bootstrap Approximation
vparam.storeMulhits_ - Switch - Store multiple equally parsimonious trees per bootstrap replicate (-mulhits)(default=0).
vparam.specifyIters_ - Integer - Number of non-ratchet iterations before each ratchet iteration (default=1)
vparam.specifyRatweight_ - Integer - Weight to add to each site selected for perturbation during ratchet (-ratchet_wgt) (default=1)
vparam.specifyRatpercent_ - Float - Percentage of informative sites selected for perturbation during ratchet (-ratchet_percent) (default=50)
vparam.turnoffRat_ -Switch - Turn off ratchet, i.e. Only use tree perturbation (-ratchet_off) (default=0)
vparam.specifyRadius_ - Integer - Maximum radius of SPR (-spr_rad) (default=6)   
vparam.specifyCutoff_ - Integer - Use top #s percentile as cutoff for selecting bootstrap candidates (-cand_cutoff) (default=10)
vparam.optBtreeoff_ - Switch - Turn off refinement step on the final bootstrap tree set (-opt_btree_off) (default=0)
vparam.nniHillclimb_ - Switch - Hill-climb by NNI instead of SPR (-nni_pars) (default=0).
vparam.uniformCost_ - Switch - Uniform cost between character states (-cost e) (default=0)
        
New Stochastic Tree Search Algorithm
vparam.specifyNumpars_ - Integer - Number of initial parsimony trees (-numpars). (default=100)
vparam.specifyToppars_ - Integer - Number of best parsimony trees (-toppars) (default=20)
vparam.specifyTreeset_ - Integer - Size of the candidate tree set (default=5)
vparam.specifyPertstrength_ - Float - Perturbation strength for randomized NNI (-pers) (default=0.5)
vparam.specifyNumstop_ - Integer - Number of unsuccessful iterations to stop (-numstop) (default=100)
vparam.specifyIterations_ - String - Run this number of iterations (-n) (default=auto)
vparam.useIqp_ - Switch - Use the IQP tree perturbation (-iqp) (default=0)
vparam.useOldiqpnni_ - Switch - Switch back to the old IQPNNI tree search algorithm (-iqpnni) (default=0)

Ultrafast Bootstrapping
vparam.useUltrafast_ - Switch - Use Ultrafast Bootstrapping  (default=0)
vparam.specifyUboots_ - Integer - Specify the number of Ultrafast bootstraps. (default=1000)
vparam.specifyMaxiters_ - Integer -  Maximum number of iterations (-nm) (default=1000)
vparam.specifyUfiters_ - Integer - Iterations for UFBoot stopping rule (-nstep) (default=100)
vparam.specifyMincorr_ - Float - Minimum correlation coefficient (-bcor) (default=0.99)
vparam.specifyRelleps_ - Float - RELL epsilon to break tie (-beps) (default=0.5)

Consensus Reconstruction
vparam.specifyMinsplit_ - Float - Min split support (-t) (default=0)
vparam.specifyBurnin_ - Integer - How many trees to discard at beginning of treefile (-bi) (no default)
vparam.writeTocontree_ - Switch - Compute consensus tree to .contree file (-con) (default=0)
vparam.writeTonexnet_ - Switch - Compute consensus network to .nex file (-net) (default=0)

Robinson-Foulds distance
vparam.alltoallRfdistance_ - Switch - Compute all-to-all RF distances of trees in treefile (-rf_all) (default=0)
vparam.computeRfadj_ - Switch - Compute RF distances of adjacent trees in treefile (-rf_adj) (default=0)

Generate Random Trees
vparam.randomTreemodel_ - Excl - Create a random tree under this model (-r)  (-r, -ru, -rcat, -rbal, -rcsg) (no default)
vparam.specifyTaxa_ -Integer - How many taxa in your random trees? (no default)
vparam.specifyminLengths_ - Integer - Min branch lengths of random trees (no default)
vparam.specifymeanLengths_ - Integer - Mean branch lengths of random trees (no default)
vparam.specifymaxLengths_ - Integer - Max branch lengths of random trees (no default

 

. Please let us know if you have any problems with the documentation.

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