Inputsection-searchstring
Enter the name of an EMBOSS program
Additionalsection-explodeboolean
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 Default value: N
Advancedsection-embossboolean
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 General
Public License scheme Default value: Y
-embassyboolean
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 General
Public License scheme Default value: Y
-showembassystring
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 General
Public License scheme
Outputsection-outfileoutfile
Default value: stdout
Htmlsection-htmltoggle
If you are sending the output to a file, this will format it for displaying as a table in a WWW
document. Default value: N
-groupsboolean
If you use this option, then only the group names will output to the file Default value: N
-colonboolean
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. Default value: N