modet: network motif discovery using expansion tree
Version: 0.1

Sabyasachi Patra - IIIT Bhubaneswar, Odisha, India
sabyasachi@iiit-bh.ac.in
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This software package is used to count the number of occurrences of subgraphs in a target network, and taking the decision on network motifs.

You can find more about it on the following url:
https://github.com/sabyasachipatra/modet

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License

This software uses the nauty program version 2.4 by Brendan McKay (http://cs.anu.edu.au/~bdm/nauty/).
Therefore, nauty's license restrictions also apply to the usage of modet.
Nauty files are included in the "nauty" directory.

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INSTALL

Just use 'make'
[Tested with Ubuntu 16.04 and GCC 8.2)

If you have any trouble compiling, please contact the author.

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VERY SHORT MANUAL

Examples of usage

COMPILE
-------
You should compile the program using make command.
make

RUN
---
You should call the program like this:
./run -m[--method] method_name -s[--size] motif_size -g[--graph] real_graph

Possible Options

 - [-s <int>] or [--size <int>]
   motif size to consider (mandatory)

 - [-g <file>] or [--graph <file>]
   File containing the graph (mandatory)

 - [-m <string>] or [--method <string>]
   Method for searching for motifs. 'method' can be: (mandatory)
   . "modet": Motif discovery using Expansion tree
   . "mdet": Motif discovery using Dynamic Expansion Tree (DET)

 - [-r <int>] or [--random <int>]
   Number of random networks to generate. (default is 0)
   Leave at zero to just compute frequency.

 - [-e <int>] or [--rexchanges <int>]
   Number of exchanges per edge on randomization. (default is 2)

 - [-t <int>] or [--tries <int>]
   Number of tries per edge on randomization. (default is 7)
   
 - [-th <int>] or [--threshold <int>]
   Threshold Frequency set as percentage of the order of the network. (default is 5)

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valid method_name: modet | mdet
valid motif_size:
		modet: 3-10
		mdet: 3-15
valid real_graph: text file containing real network in simple interaction format(SIP) is acceptable

example: ./run -m modet -s 3 -g sample.txt

example of SIP format (undirected graph)
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node node weight
1     6     1
1     7     1
2     4     1
2     3     1
3     5     1
4     5     1
5     7     1
6     7     1

Note: Above network contains 7 nodes and 8 edges