pupudu/HMM-CpG-Island

A hidden marcov model to detect CpG Islands on a string of neucleotides

1) Use,
 "javac CpGIsland.java" 
on commandline to compile program.(In case the pre-compiled CpGIsland.class file is not found)

2) To run the file, execute,
	"java CpGIsland <fileName>"

Eg- "java CpGIsland input.txt"
Note - If <fileName> is empty, program will assume name as "input.txt"

3) Read java file to read comments on the implementation of the HMM and the Viterbi Decoding