This Graph9 program does clustering based on adjacency matrix. An adjacency matrix representation of a graph
is a V-by-V array of Boolean values, with the entry in row v and column w defined to be 1 if there is an edge
connecting vertex v and vertex w in the graph, and to be 0 otherwise.

Connected graph -- A graph which each node can reach all other nodes via edges.

Cluster of genes -- A biological term refering to a connected graph of genes.

Bridges -- In Computer Science sense it should be called articulation point, but in the field of biology
we use the term "bridge" to refer to the same thing. Bridges are nodes that if removed, would generate
disconnected graphs.

Right after calling Graph9 from the command line, it will ask you for two input file, which are the node
file and the matrix file described above. Then it will ask for a cutoff value. The cutoff value determines
whether an edge is strong enough to be considered an edge in graphs. An edge with strength value less than
the cutoff value will be considered non-existent.

The format of each line in the node file is: NodeName

The format of each line in the matrix file is: NodeA NodeB strengthValue