
                                  seealso 



Function

   Finds programs sharing group names

Description

   This program takes the name of an existing program in EMBOSS (or a
   program in one the associated EMBASSY packages) and gives a list of
   the programs which share some functionality with it.

   It does this by noting the functional groups that the program belongs
   to and reporting any programs which share those functional groups.

   The functional groups of a program are set in the ACD file (this is
   the part of the program in the EMBOSS system which specifies the
   required parameters, some help on the parameters, the one-line
   description of the program, etc.) Normally the names of the groups are
   fairly specific, such as: "NUCLEIC COMPOSITION", resulting in the
   reporting of only a tightly restricted set of other programs also
   dealing with the analysis of "NUCLEIC COMPOSITION". The '-explode'
   qualifier will increase the number of groups that the program belongs
   to 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. In other words, use the '-explode'
   qualifier to decrease the specificity of the search.

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

Usage

   Here is a sample session with seealso


% seealso 
Finds programs sharing group names
Program to search for: matcher

SEE ALSO
seqmatchall      All-against-all comparison of a set of sequences
supermatcher     Match large sequences against one or more other sequences
water            Smith-Waterman local alignment
wordfinder       Match large sequences against one or more other sequences
wordmatch        Finds all exact matches of a given size between 2 sequences


Command line arguments

   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 is
                                  accepted)
   -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 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 dying program messages

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

   None.

References

   None.

Warnings

   None.

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      Reads ABI file and display the trace
   cirdna       Draws circular maps of DNA constructs
   infoalign    Information on a multiple sequence alignment
   infoseq      Displays some simple information about sequences
   lindna       Draws linear maps of DNA constructs
   pepnet       Displays proteins as a helical net
   pepwheel     Shows protein sequences as helices
   prettyplot   Displays aligned sequences, with colouring and boxing
   prettyseq    Output sequence with translated ranges
   remap        Display sequence with restriction sites, translation etc
   showalign    Displays a multiple sequence alignment
   showdb       Displays information on the currently available databases
   showfeat     Show features of a sequence
   showseq      Display a sequence with features, translation etc
   sixpack      Display a DNA sequence with 6-frame translation and ORFs
   textsearch   Search sequence documentation. Slow, use SRS and Entrez!
   tfm          Displays a program's help documentation manual
   whichdb      Search all databases for an entry
   wossname     Finds programs by keywords in their one-line documentation

Author(s)

   Gary Williams (gwilliam © 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
