2 probcons [OPTION]... [MFAFILE]...
5 Align sequences in MFAFILE(s) and print result to standard output
8 use CLUSTALW output format instead of MFA
10 -c, --consistency REPS
11 use 0 <= REPS <= 5 (default: 2) passes of consistency transformation
13 -ir, --iterative-refinement REPS
14 use 0 <= REPS <= 1000 (default: 100) passes of iterative-refinement
16 -pre, --pre-training REPS
17 use 0 <= REPS <= 20 (default: 0) rounds of pretraining
20 generate all-pairs pairwise alignments
23 use Viterbi algorithm to generate all pairs (automatically enables -pairs)
26 report progress while aligning (default: off)
29 write annotation for multiple alignment to FILENAME
32 compute EM transition probabilities, store in FILENAME (default: no training)
35 also reestimate emission probabilities (default: off)
37 -p, --paramfile FILENAME
38 read parameters from FILENAME (default: )
41 print sequences in alignment order rather than input order (default: off)