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CP specifications


Unique identifier OMICS_29984
Name CP
Alternative name Cluster Picker
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A set of aligned sequences and a newick tree built from those same sequences, with support values on the nodes.
Input format FASTA
Output data A log file listing for each cluster: cluster number, cluster size, maximum genetic distance within the cluster, support value and tip names, and a file in which sequence names are preceded by their cluster number.
Output format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.5
Stability Stable
Java Running Environment
Maintained Yes




No version available



  • person_outline Manon Ragonnet-Cronin
  • person_outline Emma Hodcroft

Publication for Cluster Picker

CP citations


HIV 1 genetic transmission networks among men who have sex with men in Kunming, China

PLoS One
PMCID: 5919538
PMID: 29698467
DOI: 10.1371/journal.pone.0196548

[…] l sequences identified in Kunming during 2010–2015, by using the neighbor-joining method based on the Tamura-Nei 93 model (). The transmission clusters were extracted from the phylogenetic tree using Cluster Picker software []. Transmission clusters were defined as those with node support thresholds greater than 90% and intra-cluster maximum pairwise genetic distances of less than 3.0% nucleotide […]


HIV 1 Infection in Cyprus, the Eastern Mediterranean European Frontier: A Densely Sampled Transmission Dynamics Analysis from 1986 to 2012

Sci Rep
PMCID: 5786036
PMID: 29374182
DOI: 10.1038/s41598-017-19080-5
call_split See protocol

[…] ) for subtype CRF02_AG.An ML tree was generated for each subtype with the GTR+4Γ nucleotide substitution model using 1,000 bootstraps, implemented in RAxML (version 8.0). The TCs were identified with Cluster Picker using a genetic distance of 0.045 as the threshold and bootstrap support of 70%. To evaluate the effects of the definition of the TC in the results, a sensitivity analysis was performed […]


Hepatitis C virus spread from HIV positive to HIV negative men who have sex with men

PLoS One
PMCID: 5749770
PMID: 29293630
DOI: 10.1371/journal.pone.0190340
call_split See protocol

[…] 57, HQ850279, M62321 and M67463) and for genotype 4d (Genbank accession numbers DQ418786, FJ462437 and EU392172) were chosen for comparison.Identification of transmission clusters was performed using Cluster Picker software with a support threshold of 0.9 and a genetic distance threshold of 0.045 []. Transmission “clusters” and “pairs” were defined as phylogenetic clades with n≥3 and n = 2 sequenc […]


Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico

J Virol
PMCID: 5752930
PMID: 29093100
DOI: 10.1128/JVI.01128-17
call_split See protocol

[…] from cohort-specific phylogenies using PATRISTIC (). gag and pol sequence clusters, defined by within-cluster patristic distances of ≤1.5% and bootstrap support values of ≥90%, were identified using Cluster Picker (The University of Edinburgh, United Kingdom) (). This genetic distance threshold has been used previously for inferring transmission clusters in chronic cohorts (). HIV genetic compart […]


Genomic analysis of bluetongue virus episystems in Australia and Indonesia

PMCID: 5701493
PMID: 29169390
DOI: 10.1186/s13567-017-0488-4

[…] substitution model for each segment, determined as above, and subtree pruning and regrafting branch-swapping. The phylogenetic robustness of each node was determined using 1000 bootstrap replicates. Cluster Picker version 1.2 [] was used to define monophyletic clades with bootstrap support values of 0.85 and a genetic distance threshold for clusters of 5%, as in previous work []. Clusters were us […]


HIV 1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach

PLoS One
PMCID: 5638258
PMID: 29023474
DOI: 10.1371/journal.pone.0185818

[…] high-risk HIV transmission to avoid additional complexity of finding spurious associations. A large study (~20,000 sequences) that evaluated the number, size, and composition of clusters detected by Cluster Picker and HIV-TRACE at six genetic distance thresholds (1%–5.3%) on three gp41 datasets showed that the optimal gp41 genetic distance threshold to distinguish linked and unlinked couples and […]


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CP institution(s)
University of Edinburgh, Edinburgh, UK; University College London, London, UK; MRC Clinical Trials Unit, London, UK; Public Health England, London, UK
CP funding source(s)
Supported by the Wellcome Trust (Grant number 092807) and the Biotechnology and Biological Science Research Council (Grant number BB/F017030/1).

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