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probcons - align multiple protein sequences and print to standard output




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.


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

generate all-pairs pairwise alignments

use Viterbi algorithm to generate all pairs (automatically enables -pairs)

-v --verbose
Report progress while aligning (default: off)

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)

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