Jacka B, Applegate T, Poon AF, Raghwani J, Harrigan PR, DeBeck K, Milloy MJ, Krajden M, Olmstead A, Joy JB, Marshall BD, Hayashi K, Pybus OG, Lima VD, Magiorkinis G, Montaner J, Lamoury F, Dore GJ, Wood E, Grebely J (2016) Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada. Journal of Hepatology 64:1247–55

Author: Jayna Raghwani

Download jar file and documentation here.


A Java program that can extract clusters defined by a threshold TMRCA from molecular clock phylogenies.

The program reads in a file that contains one or more time-scaled phylogenies (e.g. a tree log file generated by BEAST). The user specifies a threshold TMRCA value, representing the age of the clusters that user wishes to extract. Program output consists of a csv file in which each row indicates a tree from the input file, followed by cluster number, and taxa names.