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probalign - multiple sequence alignment using partition function posterior probabilities…  more info»

probalign.1.gz

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  nucleo‐
              tide data mode)).

       -score_matrix, --score_matrix

              Sets  the type of scoring matrix used to calculate the
              posterior probabilities (default:  gonnet_160,  repre‐
              senting gonnet 160, refer README for details)

       -go, --gap-open

              This option can be used to specify the gap open param‐
              eter. 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 col‐
              umns as a new sequence named  Posterior  Probabilities
              (The probability values are scaled to be between inte‐
              gers between 0 and 9).



probalign 1.4                 May 2011                  PROBALIGN(1)
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