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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

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