Automated analysis of phylogenetic clusters

UK HIV Drug Resistance Database, Manon Ragonnet-Cronin, Emma Hodcroft, Stéphane Hué, Esther Fearnhill, Valerie Delpech, Andrew Leigh Brown, Samantha Lycett

Research output: Contribution to journalArticlepeer-review

Abstract

As sequence data sets used for the investigation of pathogen transmission patterns increase in size, automated tools and standardized methods for cluster analysis have become necessary. We have developed an automated Cluster Picker which identifies monophyletic clades meeting user-input criteria for bootstrap support and maximum genetic distance within large phylogenetic trees. A second tool, the Cluster Matcher, automates the process of linking genetic data to epidemiological or clinical data, and matches clusters between runs of the Cluster Picker.
Original languageEnglish
Article number317
JournalBMC Bioinformatics
Volume14
DOIs
Publication statusPublished - 2013

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