A short manual for running Sprit. 

Sprit requires java 5 or higher to be installed.

Sprit requires trees to be in phylip format i.e.

(b,(a,(g,(h,(d,(e,f))))));

There should be only one tree per file. Sprit takes two tree files as input. 

The two trees need to have the same set of taxa be rooted and have no multifurcations. 

The software is packaged in sprit.jar and is executed as follows. 

>java -jar sprit.jar

The above command will print the available options. 

Options: 

>java -jar sprit.jar treeFile1 treeFile1 X Y Z W
 
X, execution time in seconds, unlimited = 0
Y, number of cpus for the software to use, all present = 0
Z, verbose, none (except SPR distance) = 0, a little (intermediate trees) = 1,
   a lot (the kitchen zink) = 2
W, mode of operation, conjectured = 0, hybrid = 1, exhaustive = 2
- Conjectured uses the minimal solvable common cluster conjecture from
  SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees.
- Hybrid uses the minimal common cluster reduction which might be 
  significantly quicker in some cases but does not guarantee finding the 
  minimum rSPR distance. 
- Exhaustive means that the whole tree is used when searching for the min rSPR.
  This will take a long time and does not as far as we can tell produce solutions
  better than conjectured mode
 
>java -jar sprit.jar treeFile1 treeFile1 200 2 0 0
 
Above command would run SPRIT for 200 seconds using 2 cpus in conjectured mode
producing no output except SPR distance