Automated analysis of phylogenetic clusters

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.

Cited by papers we hold 8

• A New HIV-1 K28E32-Reverse Transcriptase Variant Associated with the Rapid Expansion of CRF07_BC among Men Who Have Sex with Men · 2022
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• Tracking the COVID-19 pandemic in Australia using genomics · 2020
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• TreeCluster: Clustering biological sequences using phylogenetic trees · 2019
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• Fast hierarchical Bayesian analysis of population structure · 2019
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• DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference · 2018
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• Porcine circovirus 2 (PCV-2) genotype update and proposal of a new genotyping methodology · 2018
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• A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation. · 2017
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• Social and Genetic Networks of HIV-1 Transmission in New York City · 2017
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