
                             EMBOSS: alignwrap
     _________________________________________________________________
   
                               Program alignwrap
                                       
Function

   Aligns a set of sequences to a seed alignment
   
Description

   This is part of Jon Ison's protein structure analysis package.
   
   This package is still being developed.
   
   Please ignore this program until further details can be documented.
   
   All further queries should go to Jon Ison. (Jon Ison)
   
Usage

   Here is a sample session with alignwrap:

% alignwrap

Command line arguments

   Mandatory qualifiers:
   -inpath             string     Directory containing the seed alignments
                                  (input)
   -extn               string     File extention of seed alignment files
                                  (input)
   -scopfamilies       string     scop families file containing the set of
                                  sequences in EMBL-like format
   -outpath            string     Directory for extended alignments (output)
   -outextn            string     File extention of extended alignment files
                                  (output)

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   -inpath Directory containing the seed alignments (input) Any string is
   accepted ./
   -extn File extention of seed alignment files (input) Any string is
   accepted .align
   -scopfamilies scop families file containing the set of sequences in
   EMBL-like format Any string is accepted An empty string is accepted
   -outpath Directory for extended alignments (output) Any string is
   accepted ./tmp/
   -outextn File extention of extended alignment files (output) Any
   string is accepted .extalign
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

Output file format

Data files

Notes

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name                      Description
   est2genome   Align EST and genomic DNA sequences
   needle       Needleman-Wunsch global alignment
   stretcher    Finds the best global alignment between two sequences
   
Author(s)

   This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)
   
History

   Written (date) - author.
   
Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
   
Comments
