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Cluster specifications


Unique identifier OMICS_01571
Name Cluster
Alternative name Cluster3
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes




No version available



  • person_outline Sarah Jane Pethybridge
  • person_outline Scot Nelson

Additional information

A version 3.0 is available at:

Publications for Cluster

Cluster citations


Study of formation of green eggshell color in ducks through global gene expression

PLoS One
PMCID: 5788541
PMID: 29377917
DOI: 10.1371/journal.pone.0191564

[…] (q-value ≤ 0.05 and |Log2 (fold change)| >1) using the DESeq R package (1.8.3). Hierarchical cluster analysis was performed for differentially expressed miRNAs with similar expression patterns using Cluster3.0 software []. Predicting the target gene of miRNA was performed with miRanda []. […]


Polycomb repressive complex 1 controls uterine decidualization

Sci Rep
PMCID: 4867636
PMID: 27181215
DOI: 10.1038/srep26061
call_split See protocol

[…] values were calculated by BioWardrobe. Differentially expressed genes were identified with DESeq2 using Padj < 0.05, fold change > 1.5 and RPKM > 3 in at least one condition. Heatmap was built using Cluster3 and JavaTreeView. Functional enrichment analysis of the differentially expressed genes was performed using ToppFun ( and AltAnalyze was used to build the network whi […]


Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

PLoS One
PMCID: 3986090
PMID: 24732211
DOI: 10.1371/journal.pone.0094449
call_split See protocol

[…] r the principal component scores of water and sediment samples separately. In addition, the numbers of reads assigned to different genera were converted into percentages, which served as an input for Cluster3 . Genera with a low relative abundance of less than 0.02% of all 22 samples were removed. The remaining genera were further normalized and centered by the mean. The complete linkage method wi […]


Telomere length kinetics assay (TELKA) sorts the telomere length maintenance (tlm) mutants into functional groups

Nucleic Acids Res
PMCID: 4041441
PMID: 24728996
DOI: 10.1093/nar/gku267
call_split See protocol

[…] All the data measured by TelQuant analysis was analysed using Excel. Clusters were made using CLUSTER3 () (∼mdehoon/software/cluster/) and viewed by the JAVA TREEVIEW program ( (). Preliminary analysis of mutants affecting known protein co […]


In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

Sci Rep
PMCID: 5378041
PMID: 24399144
DOI: 10.1038/srep03587

[…] eads was performed by RDP classifier against Silva108 with a bootstrap confidence of 50%. The relative abundance of reads assigned to different taxa served as the input for generating a heatmap using Cluster3. Taxa with small differences in relative abundance among samples were filtered out by applying a threshold divergence of 0.5%. The remaining taxa were then normalized and centered by mean. A […]


Overlapping genes of Aedes aegypti: evolutionary implications from comparison with orthologs of Anopheles gambiae and other insects

BMC Evol Biol
PMCID: 3689595
PMID: 23777277
DOI: 10.1186/1471-2148-13-124

[…] unless stated otherwise. Cluster analyses of gene pairs based on overlapping or non-overlapping structures across genomes were based on average correlation of city-block distance estimated using the Cluster3 program []. The phylogenetic analyses were performed by neighbor-joining method using MEGA4 []. The evolutionary distances were in the units of the number of base substitutions per site; and […]


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Cluster institution(s)
College of Tropical Agriculture and Human Resources, Department of Tropical Plant and Soil Sciences, University of Hawai‘i at Mãnoa, Honolulu, HI, USA; AQUASoft Inc., Bucharest, Romania; Cornell University, School of Integrative Plant Science, Section of Plant Pathology & Plant-Microbe Biology, Cornell University, Geneva, NY, USA
Cluster funding source(s)
Supported by the United States Department of Agriculture, National Institute of Food and Agriculture (USDA – NIFA) Hatch project NYG-625424, managed by the New York State Agricultural Experiment Station, Cornell University, Geneva, NY, and USDA-NIFA Hatch project HAW08036-H (Accession no. 1010616) administered by the College of Tropical Agriculture and Human Resources, University of Hawai‘i at Mānoa.

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