
                              EMBOSS: plotcon
     _________________________________________________________________
   
                                Program plotcon
                                       
Function

   Plots the quality of conservation of a sequence alignment
   
Description

   Displays a graphical representation of the similarity along a set of
   aligned sequences.
   
   The similarity is calculated by moving a window of a specified length
   along the aligned sequences. Within the window, the similarity of any
   one position is taken to be the average of all the possible pairwise
   scores of the bases or residues at that position. The pairwise scores
   are taken from the specified similarity matrix. The average of the
   position similarities within the window is plotted.
   
   The program is useful for determining where the quality of alignments
   is good or bad.
   
Usage

   Here is a sample session with plotcon:

% plotcon -sformat msf alignment.msf

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-msf]               seqset     File containing a sequence alignment
   -winsize            integer    Number of columns to average alignment
                                  quality over. The larger this value is, the
                                  smoother the plot will be.
*  -graph              xygraph    Graph type
*  -outfile            outfile    Display as data

   Optional qualifiers:
   -scorefile          matrix     Comparison matrix file

   Advanced qualifiers:
   -data               bool       Output the match data to a file instead of
                                  plotting it

   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
   [-msf]
   (Parameter 1) File containing a sequence alignment Readable sequences
   Required
   -winsize Number of columns to average alignment quality over. The
   larger this value is, the smoother the plot will be. Any integer value
   4
   -graph Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png EMBOSS_GRAPHICS value, or x11
   -outfile Display as data Output file <sequence>.plotcon
   Optional qualifiers Allowed values Default
   -scorefile Comparison matrix file Comparison matrix file in EMBOSS
   data path EBLOSUM62 for protein
   EDNAFULL for DNA
   Advanced qualifiers Allowed values Default
   -data Output the match data to a file instead of plotting it Yes/No No
   
Input file format

   A set of gapped, aligned sequences.
   
Output file format

   A graph of the quality of the alignment is plotted.
   
Data files

   It reads in the specified similarity matrix.
   
   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.
   
   To see the available EMBOSS data files, run:
   
% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".
   
   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata
       
Notes

   None.
   
References

   None.
   
Warnings

   If you give it a set of unaligned sequences, it will plot the (poor!)
   quality of these as if they were aligned.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name                        Description
   emma         Multiple alignment program - interface to ClustalW program
   infoalign    Information on a multiple sequence alignment
   prettyplot   Displays aligned sequences, with colouring and boxing
   showalign    Displays a multiple sequence alignment
   tranalign    Align nucleic coding regions given the aligned proteins
   
Author(s)

   This application was written by Tim Carver (tcarver@hgmp.mrc.ac.uk)
   
History

   Written (Sept 2000) - Tim Carver.
   
Target users

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