'\" t .\" Title: COMPLEX .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "COMPLEX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" complex \- Find the linguistic complexity in nucleotide sequences .SH "SYNOPSIS" .HP \w'\fBcomplex\fR\ 'u \fBcomplex\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-lwin\ \fR\fB\fIinteger\fR\fR \fB\-step\ \fR\fB\fIinteger\fR\fR \fB\-jmin\ \fR\fB\fIinteger\fR\fR \fB\-jmax\ \fR\fB\fIinteger\fR\fR \fB\-omnia\ \fR\fB\fItoggle\fR\fR \fB\-sim\ \fR\fB\fIinteger\fR\fR \fB\-freq\ \fR\fB\fIboolean\fR\fR \fB\-print\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-ujtablefile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBcomplex\fR\ 'u \fBcomplex\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcomplex\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-lwin\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-step\fR \fIinteger\fR .RS 4 Displacement of the window over the sequence Default value: 5 .RE .PP \fB\-jmin\fR \fIinteger\fR .RS 4 Default value: 4 .RE .PP \fB\-jmax\fR \fIinteger\fR .RS 4 Default value: 6 .RE .SS "Advanced section" .PP \fB\-omnia\fR \fItoggle\fR .RS 4 Calculate over a set of sequences Default value: N .RE .PP \fB\-sim\fR \fIinteger\fR .RS 4 Calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases .RE .PP \fB\-freq\fR \fIboolean\fR .RS 4 Execute the simulation of a sequence based on the base frequency of the original sequence Default value: N .RE .SS "Output section" .PP \fB\-print\fR \fIboolean\fR .RS 4 Generate a file named UjTable containing the values of Uj for each word j in the real sequence(s) and in any simulated sequences Default value: N .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-ujtablefile\fR \fIoutfile\fR .RS 4 Default value: complex\&.ujtable .RE .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP complex is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp