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PROBALIGN Version 1.4 (Nov 2010)
Written by Satish Chikkagoudar and Usman Roshan using PROBCONS 1.1
code (written by Chuong Do) and based upon probA (written by Ulrike
Muckstein).
-----------------------------------------------------------------
PROBALIGN has been made freely available as PUBLIC DOMAIN
software and hence is not subject to copyright in the United
States. This system and/or any portion of the source code
may be used, modified, or redistributed without restrictions.
PROBALIGN is distributed WITHOUT WARRANTY, express or implied.
The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for
loss due to reliance on the program.
-----------------------------------------------------------------
PROBALIGN aligns inputted sequences and displays the output to the
screen.
USAGE:
------
./probalign [file containing sequences in MFA format]
[-T temperature]
[-v|--verbose]
[-a|--alignment-order]
[-clustalw]
[-prot|-nuc]
[-go|--gap-open gap_open]
[-ge|--gap-extension gap_ext]
[-score_matrix scoring_matrix]
OPTION DETAILS:
---------------
-T
This option is used to specify the thermodynamic temperature.
( Default: 5
when -prot option is used: 5
when -nuc option is used : 1 ).
-score_matrix
This option can be used to specify the scoring matrix.
The values that can be entered under this option are:
gonnet_160 = Gonnet 160 [DEFAULT]
nuc_simple = Identity nucleotide scoring matrix [DEFAULT for RNA/DNA]
-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)
-go, --gap-open
This option can be used to specify the gap open parameter. 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 extend parameter. 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 MODE]
-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).
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