NAME

       probcons - align multiple protein sequences and print to standard output

SYNOPSIS

       probcons [OPTION] [MFAFILE] [MFAFILE]

DESCRIPTION

       probcons is a tool for generating multiple alignments of protein sequences. Using a
       combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS
       has achieved the highest accuracies of all alignment methods to date. On the BAliBASE
       benchmark alignment database, alignments produced by PROBCONS show statistically
       significant improvement over current programs, containing an average of 7% more correctly
       aligned columns than those of T-Coffee, 11% more correctly aligned columns than those of
       CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN.

       probcons aligns sequences provided in MFA format. This format consists of multiple
       sequences. Each sequence in MFA format begins with a single-line description, followed by
       lines of sequence data. The description line is distinguished from the sequence data by a
       greater-than (“>”) symbol in the first column.

OPTIONS

       -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)

SEE ALSO

       •   You can find more information in the manual of ProbCons, which is located in
           /usr/share/doc/probcons/manual.pdf in Debian systems.

       •   An experimental version of ProbCons compiled with parameters estimated via
           unsupervised training on BRAliBASE, probcons-RNA(1), is also distributed in the
           ProbCons Debian package.

       •    pc-makegnufile(1), pc-compare(1), pc-project(1), which are distributed separately in
           the probcons-extra package.

REFERENCE

       Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS:
       Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.

AUTHORS

       Chuong Do <chuongdo@cs.stanford.edu>
           Wrote probcons in collaboration with Michael Brudno in the research group of Serafim
           Batzoglou, Department of Computer Science, Stanford University.

       Charles Plessy <charles-debian-nospam@plessy.org>
           Wrote this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       This program and its manpage are in the public domain.