
                                    mse 



Function

   Multiple Sequence Editor

Description

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Algorithm

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Usage

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     File containing a sequence alignment

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -tmpdir             outdir     Temp directory

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) File containing a sequence alignment Readable set of
   sequences Required
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -tmpdir Temp directory Output directory /tmp

Input file format

   mse reads any normal sequence USAs.

Output file format

   mse outputs a graph to the specified graphics device. outputs a report
   format file. The default format is ...

Data files

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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
   emma         Multiple alignment program - interface to ClustalW program
   infoalign    Information on a multiple sequence alignment
   plotcon      Plots the quality of conservation of a 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 program is an EMBOSS conversion of a program written by Will
   Gilbert as part of his MSE package.

History

Target users

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