:: DESCRIPTION
DomClust is an effective tool for orthologous grouping in multiple genomes, which is a crucial first step in large-scale comparative genomics.
::DEVELOPER
Ikuo Uchiyama (uchiyama@nibb.ac.jp)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2006 Jan 25;34(2):647-58.
Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes.
Uchiyama I.
:: DESCRIPTION
ESPRIT-Tree is a software for hierarchical clustering analysis of massive sequence data.
::DEVELOPER
Bioinformatics Laboratory, SUNY Buffalo
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Y. Cai and Y. Sun
ESPRIT-Tree: Hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasilinear Time,
Nucleic Acids Research, vol. 39, no. 14, e95, 2011. (impact factor: 7.8)
:: DESCRIPTION
HHCompare is a pipeline for HMM-HMM comparison based hierarchial clustering and analysis of potential paralogues in sequence set.
::DEVELOPER
Ranko Gacesa, King’s College London
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gene duplications are extensive and contribute significantly to the toxic proteome of nematocysts isolated from Acropora digitifera (Cnidaria: Anthozoa: Scleractinia).
Gacesa R, Chung R, Dunn SR, Weston AJ, Jaimes-Becerra A, Marques AC, Morandini AC, Hranueli D, Starcevic A, Ward M, Long PF.
BMC Genomics. 2015 Oct 13;16(1):774. doi: 10.1186/s12864-015-1976-4.
:: DESCRIPTION
pvclust is an R package for assessing the uncertainty in hierarchical cluster analysis. For each cluster in hierarchical clustering, quantities called p-values are calculated via multiscale bootstrap resampling. P-value of a cluster is a value between 0 and 1, which indicates how strong the cluster is supported by data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pvclust: an R package for assessing the uncertainty in hierarchical clustering.
Suzuki R, Shimodaira H.
Bioinformatics. 2006 Jun 15;22(12):1540-2. Epub 2006 Apr 4.
:: DESCRIPTION
CLAG (for CLusters AGgregation) is an unsupervised non hierarchical clustering algorithm designed to cluster a large variety of biological data and to provide a clustered matrix and numerical values indicating cluster strength.
::DEVELOPER
Laboratory of Computational and Quantitative Biology(LCQB)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2012 Aug 8;13:194. doi: 10.1186/1471-2105-13-194.
CLAG: an unsupervised non hierarchical clustering algorithm handling biological data.
Dib L1, Carbone A.
:: DESCRIPTION
pcaReduce is a novel agglomerative clustering method to generate a cell state hierarchy where each cluster branch is associated with a principal component of variation that can be used to differentiate two cell states.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
pcaReduce: hierarchical clustering of single cell transcriptional profiles.
Žurauskienė J, Yau C.
BMC Bioinformatics. 2016 Mar 22;17(1):140. doi: 10.1186/s12859-016-0984-y.
:: DESCRIPTION
BHC is an R/Bioconductor port of the fast novel algorithm for Bayesian agglomerative hierarchical clustering.
::DEVELOPER
Warwick Systems Biology Centre
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics 2009, 10:242
R/BHC: fast Bayesian hierarchical clustering for microarray data
Richard S Savage et al.
:: DESCRIPTION
GDHC (General Dependency Hierarchical Clustering) is a method of hierarchical clustering for high throughput data. Nonlinear relations exist between features of high-throughput data. They reflect critical regulation patterns in the biological system. Clustering based on both linear and nonlinear relations in high throughput data is hampered by the high dimensionality and high noise level in the data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):1080-5. doi: 10.1109/TCBB.2013.99.
Hierarchical clustering of high-throughput expression data based on general dependences.
Yu T, Peng H
:: DESCRIPTION
DBC454 is a density-based hierarchical clustering algorithm.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 May 15;29(10):1268-74. doi: 10.1093/bioinformatics/btt149. Epub 2013 Mar 28.
Density-based hierarchical clustering of pyro-sequences on a large scale–the case of fungal ITS1.
Pagni M, Niculita-Hirzel H, Pellissier L, Dubuis A, Xenarios I, Guisan A, Sanders IR, Goudet J, Guex N.
:: DESCRIPTION
HappieClust is an approximate version of agglomerative hierarchical clustering. When performing the standard full agglomerative hierarchical clustering, each pair of objects must be inspected to evaluate similarity. This is very time-consuming for large numbers of objects and/or complicated similarity measures. HappieClust performs agglomerative hierarchical clustering with partial information, not requiring all pairwise similarities to be known. HappieClust is further able to use similarity heuristics to carefully choose a subset of pairs for which the similarities are evaluated.
::DEVELOPER
Meelis Kull, Jaak Vilo
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
M. Kull, J. Vilo. .
Fast approximate hierarchical clustering using similarity heuristics.
BioData Mining 2008, 1:9 (22 September 2008)
