man complex (1): Find the linguistic complexity in nucleotide sequences

SYNOPSIS

complex -sequence seqall -lwin integer -step integer -jmin integer -jmax integer -omnia toggle -sim integer -freq boolean -print boolean -outfile outfile -ujtablefile outfile -outseq seqoutall
complex -help

DESCRIPTION

complex

is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Nucleic:Composition" command group(s).

OPTIONS

Input section

-sequence seqall

-lwin integer

: Default value: 100

-step integer

: Displacement of the window over the sequence Default value: 5

-jmin integer

: Default value: 4

-jmax integer

: Default value: 6

Advanced section

-omnia toggle

: Calculate over a set of sequences Default value: N

-sim integer

: Calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases

-freq boolean

: Execute the simulation of a sequence based on the base frequency of the original sequence Default value: N

Output section

-print boolean

: 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

-outfile outfile

-ujtablefile outfile

: Default value: complex.ujtable

-outseq seqoutall

BUGS

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).

AUTHOR

Debian Med Packaging Team <[email protected]>

: Wrote the script used to autogenerate this manual page.

COPYRIGHT

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.