Run
$ make 
to compile. This generates 5 executable programs in the working folder
./BLOSUM
./GloAlign
./RBLAST
./MSA
./CoupleEnergy

For help, type "-h" after each program name
e.g.
$ ./BLOSUM -h

The package comes with the following sample files

test.sampleseq.fasta 
	A sample fasta file with 22 protein sequences, among which polymorphisms on position 9 "E/H", 22 "F/K", 46 "R/T"  are coupled [For position 9 and 22, 8 'E's comes with 'F', and 12 'H's comes with 'K']. Similarly, position 33 "G/Y" and position 58 "G/L" are coupled. These coupling sites were successfully captured by ./CoupleEnergy 

test.Res.msa
	A multiple sequence alignment result file. Try "$ ./CoupleEnergy -f test.Res.msa"

Report any error to
Ruan,Xiaoyang
ruansun@163.com