PROBALIGN(1) User Commands PROBALIGN(1)
NAME
probalign - Align sequences in MFAFILE(s) and print result to standard output
DESCRIPTION
PROBALIGN Version 1.4 (Nov 2010) aligns multiple protein sequences and prints to the standard output. Written by Satish Chikkagoudar and
Usman Roshan using code from PROBCONS version 1.1 (written by Chuong Do) and based upon probA (written by Ulrike Muckstein).
PROBALIGN 1.4 comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions.
See the README file for details.
Usage:
probalign [OPTION]... [MFAFILE]...
Description:
Align sequences in MFAFILE(s) and print result to standard output
-clustalw
use CLUSTALW output format instead of MFA
-v, --verbose
report progress while aligning (default: off)
-a, --alignment-order
print sequences in alignment order rather than input order (default: off)
-T, -temperature
Sets the thermodynamic temperature parameter
(default: 5 (for protein data mode), 1 ( for nucleotide data mode)).
-score_matrix, --score_matrix
Sets the type of scoring matrix used to calculate the posterior probabilities (default: gonnet_160, representing gonnet 160, refer
README for details)
-go, --gap-open
This option can be used to specify the gap open parameter. The default for Gonnet 160 (protein) is 22 and nucleotide (simple matrix)
is 4.
-ge, --gap-extension
This option can be used to specify the gap extension parameter. The default for Gonnet 160 (protein) is 1 and nucleotide (simple
matrix) is 0.25.
-nuc
Specify this option to indicate that inputted sequences are nucleotide sequences
-prot
Specify this option to indicate that inputted sequences are protein sequences [DEFAULT]
-showPP
Outputs the posterior probabilities of alignment columns as a new sequence named Posterior Probabilities (The probability values are
scaled to be between integers between 0 and 9).
probalign 1.4 May 2011 PROBALIGN(1)
