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)