Picking and Describing HIV Clusters in Phylogenetic Trees

A tool combination for the analysis of phylogenetic clusters of nucleotide sequences

The most recent versions of the ClusterPicker and ClusterMatcher are always on our GitHub page (right-click a file and 'Save link as' to download).

Download program ClusterPickerGUI_1.2.3.jar (GUI version) Download program ClusterPicker_1.2.3.jar (command line version) Download manual ClusterPicker.pdf

Download program ClusterMatcher.jar Download manual ClusterMatcher.pdf Download Tutorial and Scripts

Description

Cluster identification strategies differ between studies and as a consequence cluster definitions vary.

The Cluster Picker identifies clusters in newick-formatted trees containing thousands of sequences within a few minutes. Cut-offs for within cluster genetic distance and bootstrap support are selected by the user.

Because many groups then look at the epidemiology of these clusters, the Cluster Matcher automatically links Cluster Picker output to spreadsheets of epidemiological data.

Associated publication

Ragonnet-Cronin M, Lycett SJ, Hodcroft E, Hue S, Fearnhill E, Dunn D, Delpech V, Leigh Brown AJ. Automated analysis of phylogenetic clusters. BMC Bioinformatics 14:317; 2013 link to journal article.

Installation

To run the Cluster Picker and Cluster Matcher, you will need Java 1.6.0 or higher. The jar file will run on PC, Mac, UNIX and LINUX operating systems.

Source Code

https://github.com/emmahodcroft/cluster-picker-and-cluster-matcher
Source code, the latest built jar files and the tutorial.

Released under GNU GLPv3.

Unless explicitly stated otherwise, all material is copyright © The University of Edinburgh.