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)