Earth mover's distance between de Bruijn graphs
First, you need to compile the FastEMD code. Go to the FastEMD sub-directory and:
In Matlab:
>> compile_FastEMD
In a linux shell:
>> make
##Usage## The script RunEMDeBruijn.m contains a Matlab function
[dist,flow]=RunFastEMDAllPairwise(file_name1,file_name2,kmer_size)
The files file_name1 and file_name2 contain the kmer_size counts (one per line, in lexicographic order). The script will return the distance dist and the flow
(a matrix of size 4^kmer_size x 4^kmer_size telling what kmer mass got moved where).
###Restrictions###
Currently, the kmer_size is restricted to 5, 6, or 7.
####Acknowledgments#### The FastEMD code is due to Ofir Pele. See the file FastEMD/README.txt