#!/bin/sh

# $1 = input trees
# $2 = "-approx" (optional: does a 4-approx instead of the default 2-approx)

java DriveWhidden -t $1 -o $1.maf $2

# don't forget to specify the -glpkpath flag, if required, to point to your glpsol executable
java NewickToDFVS -m $1.maf < $1

java Aaf2network $1 $1.maf.aaf