GTP

A fork of Megan Owen and Scott Provan's java implementation of their GTP algorithm for calculating the geodesic distance between phylogenetic trees, from this paper. The original code only allowed for all-all comparisons, this version is modified to allow row-wise comparisons - i.e. the first tree in a file against all other trees. This is activated with the '-r' switch.

Installation

First compile the sources:

javac polyAlg/*.java distanceAlg1/*.java

Then pack the jar file:

jar cfm gtp.jar manifest.txt polyAlg/*.class distanceAlg1/*.class

Or run the Makefile by typing:

make

You can clean up the compiled classes with:

make clean

Usage

Run with java -jar gtp.jar [options] trees_file.

--help outputs this:

Command line syntax:
gtp [options] treefile
Optional arguments:
	 -d 	 double check results, by computing each distance with the target tree as the starting tree and vice versa; default is false
	 -h || --help 	 displays this message
	 -n 	 normalize (vector of the lengths of all edges has length 1)
	 -o <outfile> 	 store the output in the file <outfile>
	 -u 	 unrooted trees (default is rooted trees)
	 -v || --verbose 	 verbose output
	 -r || --row 	 Compute geodesics between the first tree in the input file and all the others (not an all-all comparison)