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COMPLEX(1e) EMBOSS Manual for Debian COMPLEX(1e)


complex - Find the linguistic complexity in nucleotide sequences


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


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).


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 can be reported to the Debian Bug Tracking system (, or directly to the EMBOSS developers (


complex is fully documented via the tfm(1) system.


Debian Med Packaging Team <>

Wrote the script used to autogenerate this manual page.


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.

05/11/2012 EMBOSS 6.4.0