                                   seealso



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Finds programs with similar function to a specified program

Description

   seealso takes the name of an EMBOSS or EMBASSY program and returns a
   list of applications in the same functional group. Application names
   and short descriptions are listed. Optionally, the output is written to
   an HTML table.

Usage

   Here is a sample session with seealso


% seealso
Finds programs with similar function to a specified program
Program to search for: matcher

SEE ALSO
seqmatchall  All-against-all word comparison of a sequence set
supermatcher Calculate approximate local pair-wise alignments of larger sequence
s
water        Smith-Waterman local alignment of sequences
wordfinder   Match large sequences against one or more other sequences
wordmatch    Finds regions of identity (exact matches) of two sequences



Command line arguments

Finds programs with similar function to a specified program
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-search]            string     Enter the name of an EMBOSS program (Any
                                  string of at least 1 characters)

   Additional (Optional) qualifiers:
   -explode            boolean    [N] The groups that EMBOSS applications
                                  belong to have two forms, exploded and not
                                  exploded. The exploded group names are more
                                  numerous and often vaguely phrased than the
                                  non-exploded ones. The exploded names are
                                  formed from definitions of the group names
                                  that start like NAME1:NAME2 and which are
                                  then expanded into many combinations of the
                                  names as: 'NAME1', 'NAME2', 'NAME1 NAME2',
                                  NAME2 NAME1'. The non-expanded names are
                                  simply like: 'NAME1 NAME2'.
                                  Using expanded group names will find many
                                  more programs which share at least some of
                                  the expanded names than using the
                                  non-exploded names and so you will get more
                                  programs reported as sharing a similar
                                  function than you will if you specify that
                                  you wish to use non-exploded names
   -outfile            outfile    [stdout] Output file name
   -html               toggle     [N] If you are sending the output to a file,
                                  this will format it for displaying as a
                                  table in a WWW document.
   -groups             boolean    [N] If you use this option, then only the
                                  group names will output to the file

   Advanced (Unprompted) qualifiers:
   -[no]emboss         boolean    [Y] If you use this option then EMBOSS
                                  program documentation will be searched. If
                                  this option is set to be false, then only
                                  the EMBASSY programs will be searched (if
                                  the -embassy option is true). EMBASSY
                                  programs are not strictly part of EMBOSS,
                                  but use the same code libraries and share
                                  the same look and feel, but are generally
                                  developed by people who wish the programs to
                                  be outside of the GNU Public Licence scheme
   -[no]embassy        boolean    [Y] If you use this option then EMBASSY
                                  program documentation will be searched. If
                                  this option is set to be false, then only
                                  the EMBOSS programs will be searched (if the
                                  -emboss option is true). EMBASSY programs
                                  are not strictly part of EMBOSS, but use the
                                  same code libraries and share the same look
                                  and feel, but are generally developed by
                                  people who wish the programs to be outside
                                  of the GNU Public Licence scheme
   -showembassy        string     If you use this option then this EMBASSY
                                  package program documentation will be
                                  searched. EMBASSY programs are not strictly
                                  part of EMBOSS, but use the same code
                                  libraries and share the same look and feel,
                                  but are generally developed by people who
                                  wish the programs to be outside of the GNU
                                  Public Licence scheme (Any string)
   -colon              boolean    [N] The groups that EMBOSS applications
                                  belong to have up to two levels, for example
                                  the primary group 'ALIGNMENT' has several
                                  sub-groups, or second-level groups, e.g.:
                                  CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL,
                                  LOCAL, MULTIPLE. To aid programs that parse
                                  the output of seealso that require the names
                                  of these subgroups, a colon ':' will be
                                  placed between the first and second level of
                                  the group name if this option is true.

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit


Input file format

Output file format

   The result is header line 'SEE ALSO' then a simple list of program
   names followed by the one-line description of the program.

   If the '-html' qualifier is used, then the result is an HTML-formatted
   table, lacking the HTML document structures such as <HTML>, <BODY>,
   </BODY>, </HTML> which the user is expected to provide as the table
   will usually be included in the middle of a larger HTML document.

Data files

   None.

Notes

   The functional group of a program is set in its ACD file; this is an
   EMBOSS system file which specifies the application command-line
   interface such as required parameters, help on the parameters, one-line
   description of the program and so on. Normally the names of the groups
   are fairly specific. For example "NUCLEIC COMPOSITION" is a small group
   of applications for nucleotide sequence composition analysis.

   The -explode qualifier will increase the number of groups that the
   program retrieves by splitting the group name at selected points to
   produce such groups as: "NUCLEIC", "NUCLEIC COMPOSITION" and
   "COMPOSITION". All programs with the exploded group names which also
   include "NUCLEIC" and "COMPOSITION" will now be reported. The result of
   this qualifier is thus a report of a larger number of programs with a
   more tenuous link to the specified program.

   The groups that the program belongs to can be output by using the
   -groups qualifier.

References

   None.

Warnings

   The (optional) HTML-formatted table output lacks the HTML document
   structures such as
   , , , . It is expected the table will be included in the middle of a
   larger HTML document.

Diagnostic Error Messages

   The error message:

FATAL ERROR: No application specified.


   is output if a non-existent program name is specified.

Exit status

   The program exits with exist status '0' unless a non-existent program
   name is specified, when the exit status is '1'.

Known bugs

   None.

See also

                   Program name                            Description
                   abiview      Display the trace in an ABI sequencer file
                   cirdna       Draws circular maps of DNA constructs
                   infoalign    Display basic information about a multiple sequence alignment
                   infobase     Return information on a given nucleotide base
                   inforesidue  Return information on a given amino acid residue
                   infoseq      Display basic information about sequences
                   lindna       Draws linear maps of DNA constructs
                   pepnet       Draw a helical net for a protein sequence
                   pepwheel     Draw a helical wheel diagram for a protein sequence
                   prettyplot   Draw a sequence alignment with pretty formatting
                   prettyseq    Write a nucleotide sequence and its translation to file
                   remap        Display restriction enzyme binding sites in a nucleotide sequence
                   showalign    Display a multiple sequence alignment in pretty format
                   showdb       Displays information on configured databases
                   showfeat     Display features of a sequence in pretty format
                   showpep      Displays protein sequences with features in pretty format
                   showseq      Displays sequences with features in pretty format
                   sixpack      Display a DNA sequence with 6-frame translation and ORFs
                   textsearch   Search the textual description of sequence(s)
                   tfm          Displays full documentation for an application
                   whichdb      Search all sequence databases for an entry and retrieve it
                   wossname     Finds programs by keywords in their short description

Author(s)

   Gary             Williams (gwilliam (c) rfcgr.mrc.ac.uk)
   MRC              Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome           Campus, Hinxton, Cambridge, CB10 1SB, UK

History

                    Written 16 June 2000 in response to a need to improve the automatic
                    construction of EMBOSS documentation web pages.

Target users

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

Comments

                    None
