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Picking and Describing HIV Clusters in Phylogenetic Trees

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




Download program ClusterPickerGUI.jar (GUI version)
Download program ClusterPicker_command.jar (command line version)
Download manual ClusterPicker.pdf


Download program ClusterMatcher.jar
Download manual ClusterMatcher.pdf



Download Tutorial

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, Hodcroft E, Hué S, Fearnhill E, Dunn D, Delpech V, Leigh Brown A and Lycett S, Automated Analysis of Phylogenetic Clusters (In Preparation).

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

http://code.google.com/p/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.