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[jabaws.git] / website / archive / binaries / mac / src / probcons / OPTIONS.TXT

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-Usage:
-       probcons [OPTION]... [MFAFILE]...
-
-Description:
-       Align sequences in MFAFILE(s) and print result to standard output
-
-       -clustalw
-              use CLUSTALW output format instead of MFA
-
-       -c, --consistency REPS
-              use 0 <= REPS <= 5 (default: 2) passes of consistency transformation
-
-       -ir, --iterative-refinement REPS
-              use 0 <= REPS <= 1000 (default: 100) passes of iterative-refinement
-
-       -pre, --pre-training REPS
-              use 0 <= REPS <= 20 (default: 0) rounds of pretraining
-
-       -pairs
-              generate all-pairs pairwise alignments
-
-       -viterbi
-              use Viterbi algorithm to generate all pairs (automatically enables -pairs)
-
-       -v, --verbose
-              report progress while aligning (default: off)
-
-       -annot FILENAME
-              write annotation for multiple alignment to FILENAME
-
-       -t, --train FILENAME
-              compute EM transition probabilities, store in FILENAME (default: no training)
-
-       -e, --emissions
-              also reestimate emission probabilities (default: off)
-
-       -p, --paramfile FILENAME
-              read parameters from FILENAME (default: )
-
-       -a, --alignment-order
-              print sequences in alignment order rather than input order (default: off)
-