seealso

seealso

seealso 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 the existing program.

Here is a sample session with seealso:

% seealso Program to search for: matcher SEE ALSO seqmatchall      Does an all-against-all comparison of a set of sequences supermatcher     Finds a match of a large sequence against one or more                   sequences water            Smith-Waterman local alignment wordmatch        Finds all exact matches of a given size between 2 sequences

Mandatory qualifiers:

[-search] (string)

Enter the name of an EMBOSS program.

Optional qualifiers (bold if not always prompted):

-explode (boolean)

The groups EMBOSS applications belong to have two forms: exploded and non- exploded. The exploded group names are more numerous and often more vaguely phrased than the non-exploded ones. The exploded names are formed from definitions of the group names that start in the form NAME1:NAME2 and are then expanded into many combinations of the names, such as: NAME1, NAME2, NAME1 NAME2, NAME2 NAME1. The non-expanded names are simply listed as: NAME1 NAME2. Using exploded group names finds many more programs that share at least some of the exploded names. More programs will be reported as sharing a similar function if you use use non-exploded names.

-outfile (outfile)

If you enter the name of a file here, this program writes the program names and brief descriptions into that file.

-html (boolean)

If you are sending the output to a file, this qualifier formats it for display as a table in a WWW document.

-prelink (string)

If you are outputting to a file in HTML format, you can make the program names into hyperlinks by setting this qualifier to be the first half of the URL. If you want the program name to be a hyperlink to the URL http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html, enter http://www.uk.embnet.org/Software/EMBOSS/Apps/ to set the first half of the URL before the program name.

-postlink (string)

If you are outputting to a file in HTML format, you can make the program names into hyperlinks by setting this qualifier to be the second half of the URL. If you want the program name to be a hyperlink to the URL: http://www.uk.embnet.org/Software/EMBOSS/Apps/programname.html, enter .html to set the second half of the URL after the program name.

-groups (boolean)

If you use this option, only the group names will output to the file.

Advanced qualifiers:

-[no]emboss (boolean)

If you use this option, EMBOSS program documentation is searched. If this option is set to be false, only the EMBASSY programs are 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. These programs are generally developed by people who want their programs to be outside of the GNU Public License scheme, i.e., they may want to charge a license fee.

-[no]embassy (boolean)

If you use this option, EMBASSY program documentation is searched. If this option is set to false, 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 want the programs to be outside of the GNU Public License scheme, i.e.,. they may want to charge a license fee.

-colon (boolean)

The groups EMBOSS applications belong to may have up to two levels For example, the primary group ALIGNMENT has several sub-groups, or second-level groups: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, and MULTIPLE. To aid programs that parse the output of seealso (and require the names of these subgroups), a colon is placed between the first and second level of the group name if this option is true.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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