This program is provided without any warranty and is under the GPL license. See the LICENSE.txt file for more information.

System requirements: A variant of UNIX, with the GNU C++ compiler ("gcc") and ("make") installed.

To complile: in the "Release" folder of the program, type
	make

Usage: in the "Release" folder, type "hsforest" with parameters described below, i.e.
	hsforest [OPTION]
Options:
	<-i> A file listing the absolute path to each decoy.
	<-R> A file listing the absolute path to each pivot decoy. Should be selected randomly.
	<-B> A file listing the absolute path to the 10 best energy decoy. The file can contain between 1 and 10 decoys.
	<-o> Output file for top decoys (sorted).
	<-r> Number of pivots to sample from pivots in pivot file. Recommend value: between 20 and 60.
	<-h> H_max value. Recommended value: half of the value of the <-r> parameter.
	<-t> Number of trees. Recommended value: between 15 and 30. 
	[-S] (Optional) Number of largest clusters to consider. Default value: 30.

This usage information is also available when typing "hsforest" without parameters.

Example:

hsforest -i my_list -R my_pivots -B 10_best -o output -r 40 -h 20 -t 20