Software

rSPR Approximation Algorithm

To use this software, type:

java -jar rsprApprox.jar treefile.nexus logfile.log

where treefile.nexus is a nexus file of trees, of which the first two trees in the file will be compared (if there's more than 2, the extras will be ignored) and logfile.log is where log and debug messages are written. When run, the program will write the rSPR approximation to the screen.

rSPR Distance and Hybrid Number Computation

All the programs are included in the tar file treeSATbeta.tar.gz.

The perl scripts are:

computeHybridwR1wR3*
computeMAF*
computeMAFwR1*

The scripts use the following java files (*.jar) that can also be called directly:


rspr.jar         
rsprWR1.jar       
treeReduction.jar
treeSatHyb.jar 
treesat.jar  
treesatWR1.jar

Each one takes the size of the forest (r), and the names of the files that contain the trees.

For example,

java -jar treeSatHyb 3 s10_t1.nexus s10_t2.nexus

There's also the source code (/src) and lots of example files (*.nexus) for testing.