Automated analysis of phylogenetic clusters

TitleAutomated analysis of phylogenetic clusters
Publication TypeJournal Article
Year of Publication2013
AuthorsRagonnet-Cronin M, Hodcroft EB, Hué S, Fearnhill E, Delpech V, Leigh Brown A.J, Lycett SJ
JournalBMC Bioinformatics
Volume14
Pagination317
Date Published2013-11
ISBN Number1471-2105
Accession Number24191891
Keywords*Cluster Analysis, *Phylogeny, Computational Biology/*methods, HIV Infections/epidemiology/virology, HIV-1/genetics, Humans, Molecular Epidemiology/*methods, Sequence Analysis, RNA
Abstract

BACKGROUND: 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. RESULTS: We explore the effect of different bootstrap and genetic distance thresholds on clusters identified in a data set of publicly available HIV sequences, and compare these results to those of a previously published tool for cluster identification. To demonstrate their utility, we then use the Cluster Picker and Cluster Matcher together to investigate how clusters in the data set changed over time. We find that clusters containing sequences from more than one UK location at the first time point (multiple origin) were significantly more likely to grow than those representing only a single location. CONCLUSIONS: The Cluster Picker and Cluster Matcher can rapidly process phylogenetic trees containing tens of thousands of sequences. Together these tools will facilitate comparisons of pathogen transmission dynamics between studies and countries.

Short TitleBMC bioinformatics
Alternate JournalBMC bioinformatics