Last common ancestor (LCA) parser for sqltable results from Hieranoid2.

You must be logged as root

apt-get install openjdk-7-jdk maven git

git clone https://github.com/mashu/SQLParser

Maven will take care of all required libraries and will place them in apprioprate jar file with dependencies.

SQLParser/
mvn package

java -jar target/sqlparser-0.0.1-SNAPSHOT-jar-with-dependencies.jar \
-o ~/pairs.out -p sequences/ -sql sqltables/ -t tree/66species.tre

Running jar without arguments prints the help.