mse

 

Function

Multiple Sequence Editor

Description

**************** EDIT HERE ****************

Algorithm

**************** EDIT HERE ****************

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

**************** EDIT HERE ****************

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
emmaMultiple alignment program - interface to ClustalW program
infoalignInformation on a multiple sequence alignment
plotconPlots the quality of conservation of a sequence alignment
prettyplotDisplays aligned sequences, with colouring and boxing
showalignDisplays a multiple sequence alignment
tranalignAlign 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.