Probcons REST

ProbCons

ProbCons is a novel tool for generating multiple alignments of protein sequences using a combination of probabilistic modeling and consistency-based alignment techniques

toolId=PROBCONS

input.infile_ - Primary Input File

vparam.runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)

vparam.sequenceType_ - Excl - Data Type
vparam.outputFormat_ - Excl - Output file format
vparam.numConsistencyReps_ - Excl - Number of passes of consistency transformation (--consistency)
vparam.numRefinementReps_ - Integer - Number of passes of iterative refinement, up to 1000 (--iterative-refinement)
vparam.numPretrainingReps_ - Integer - Number of rounds of pretraining, up to 20 (--pre-training)
vparam.pairwise_ - Switch - Generate only pairwise alignments? (-pairs)
vparam.viterbi_ - Switch - Use Viterbi decoding (-viterbi)
vparam.writeAnnotation_ - Switch - Write annotation for multiple alignment (-annot)
vparam.writeTraining_ - Switch - Write EM transition probabilities (--train)
vparam.paramsFile_ - InFile - Trained ProbCons parameter file (--paramfile)

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