PROBCONS
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
infile_ - Primary Input File
sequenceType_ - Excl - Data Type
outputFormat_ - Excl - Output file format
outputMFAFile_ - OutFile -
outputMFAPairwise_ - Results -
outputClustalWFile_ - OutFile -
outputClustalWPairwise_ - Results -
numConsistencyReps_ - Excl - Number of passes of consistency transformation (--consistency)
numRefinementReps_ - Integer - Number of passes of iterative refinement, up to 1000 (--iterative-refinement)
numPretrainingReps_ - Integer - Number of rounds of pretraining, up to 20 (--pre-training)
pairwise_ - Switch - Generate only pairwise alignments? (-pairs)
viterbi_ - Switch - Use Viterbi decoding (-viterbi)
writeAnnotation_ - Switch - Write annotation for multiple alignment (-annot)
annotationResults_ - Results -
writeTraining_ - Switch - Write EM transition probabilities (--train)
trainingResults_ - Results -
paramsFile_ - InFile - Trained ProbCons parameter file (--paramfile)