Cluster-graph

To compile on a Unix/Linus machine, make sure these are in the same directory:
--main.c
--cluster.h
--cluster.c
--condensed.c
--hashtbl.c
--hashtbl.h
--Makefile

Type 'make'.

To run, you will need to input 1) a sequence file, and 2) an sfold 'sample_1000.out' file. Included in the repository is a sequence file and a sample_1000 file from ecoli 5S that may be used to run the program.

Type './main [seq file] [sample file] [options]' to run.

Common options:

-t [percent] = filter out all helix classes that occur less than [percent] number of times (default 10)
-q [percent] = filter out all profiles that occur less than [percent] number of times (default 2)
-v = verbose output
-g = disable graph making component of program (if just interested in helix and profile stats)
-o [file name] = produces the output dot file called [file name]; otherwise, output is called 'cluster.dot'