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).