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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