ArticleBMC bioinformatics2013
Automated analysis of phylogenetic clusters.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 244 papers, 1 of them a synthesis that pooled it.
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Who cites it
244 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Prevalence and spatiotemporal dynamics of HIV-1 Circulating Recombinant Form 03_AB (CRF03_AB) in the Former Soviet Union countries.PloS one · 2020Pooled it
- Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa.Viruses · 2022Trial
- Trial
- Prevalence and Phylogenetic Characterization of Hepatitis C Virus Among Indian Men Who Have Sex With Men: Limited Evidence for Sexual Transmission.The Journal of infectious diseases · 2020Trial
- Trial
- Discovering New Orthologous Groups with P-COGs.Biochemical genetics · 2026Article
- Genomic epidemiology and phylogeographic reconstruction of West Nile virus 2 in Italy from 2011 to 2023.One health (Amsterdam, Netherlands) · 2026Article
- Emerging Trends in HIV-1 Sub-Subtype A6 in Belgium: Transmission Dynamics, Drug Resistance, and Subtyping Tool Evaluation.Viruses · 2026Article
- Beyond labels: current sequencing data do not support standardized porcine circovirus 3 (PCV3) genotypes.BMC veterinary research · 2026Article
- Men who have sex with men newly diagnosed with HIV-1 in Portugal (2023-2024): a comparative analysis of transmission clusters between migrants and non-migrants.Scientific reports · 2026Article
- Invasive Group A Streptococcal Disease in Persons Experiencing Postpandemic Homelessness in Canada.JAMA network open · 2026Article
- A transmission relationship investigation of HIV infection through male-to-male sex among a case of left-behind children with heterosexual orientation in Zhejiang Province of China.Frontiers in public health · 2026Article
- Global spread and evolutionary trajectories of HIV-1 CRF01_AE: Insights from phylogenetic analysis.PloS one · 2026Article
- Beyond traditional outbreak investigation: Using genomic data for enhanced detection of COVID-19 disease clusters in Utah.PloS one · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- Unexpectedly low prevalence of hepatitis delta virus infection in Southern Viet Nam.Scientific reports · 2025Article
- Genetic evolution and alterations in pathogenicity of highly pathogenic porcine reproductive and respiratory syndrome virus.Virulence · 2025Article
- An Assessment of Regional Genetic Diversity of HIV-1.Viruses · 2025Article
- Genomic trends and emerging antimicrobial resistance inMicrobiology spectrum · 2025Article
- T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters.PLoS computational biology · 2025Article
184 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
backgroundAs 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.
resultsWe 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.
conclusionsThe 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.