SYNOPSIS
- probcons [OPTION] [MFAFILE] [MFAFILE]
DESCRIPTION
probcons
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)
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 <[email protected]>
- Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.
Charles Plessy <[email protected]>
- Wrote this manpage in DocBook XML for the Debian distribution.
COPYRIGHT
This program and its manpage are in the public domain.