### ABSTRACT

Full Article

### README

Usage:

Finding cliques in an undirected, unit-weighted graph:

CLCL -i graph -n num_of_nodes [-c clique_size_cutoff] [-e connectivity_cutoff]

'-i' specify the graph to be processed by the algorithm. The graph is represented

by a n-by-n binary matrix, where a '1' in the matrix indicates that the corresponding

vertices are connected, and a '0' otherwise. DO NOT INCLUDE HEADER IN THE MATRIX!

'-n' specify the number of nodes in the graph, which is expected to be a positive

integer.

'-c' specify the minimum number of nodes in the output clique. If a clique has less

nodes that this cutoff, it will not be output. The default value is 3.

'-e' specify the connectivity cutoff for merging (please see the article for detail).

The default value is 0.4.

Example: CLCL -i Test_Graph -n 100

The outputs are a number of rows of tab-delimited numbers. Each row represents a clique,

and the tab-delimited numbers represents nodes in the clique. The number is the row/column

index of the node in the input graph. MAKE SURE A CORRESPONDENCE LIST IS MAINTAINED

CORRECTLY TO MAP BACK THE CLIQUES!

### DOWNLOADS

Supplementary information

Performance of clustering on all families in the Rfam data set

Additional_File_1

Clustering results of RNA elements in Drosophila 3'-UTR

Additional_File_2

Differential expression of each cluster

Additional_File_3

Other companion information

The entire Rfam data set and raw clustering file

Companion_RfamRawClustering.pdf

Original FlyAtlas T-test results used to generate Additional file 3

FlyAtlas_Ttest