probalign - Align sequences in MFAFILE(s) and print result to
standard output
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.
- probalign [OPTION]... [MFAFILE]...
- 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).