INSTALLATION

Type ./install to install NDComplex.

INPUT

A file that specifies a protein interaction in each row that contains two
proteins separated by a space or a tab.

USAGE
 
ndcomplex -i input_file [options]
 
options:
 
        -h display this help and exit
        -i input_file
        -o output_file (default: input_file.t<val>.c<val>.d<val>.s<val>.out)
        -t similarity threshold during computation of neighborhood density
           (default: 0.3)
        -c occurrence threshold during computation of neighborhood density
           (default: 3)
        -d density threshold during computation of predicted complexes in
           regions with low neighborhood density (default: 0.7)
        -s similarity threshold during computation of predicted complexes in
           regions with high neighborhood density (default: 0.2)

EXAMPLE

ndcomplex -i network -t 0.3 -c 3 -d 0.7 -s 0.2

creates the output file network.t0.3.c3.d0.7.s0.2.out.

OUTPUT

Each line contains one predicted complex that is specified by '>' followed by a
list of proteins.