Get 1000 Hours free
On the UCSD Supercomputer
Start Your TrialThis 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.