:: DESCRIPTION
DNACLUST is a tool for clustering millions of short DNA sequences. The clusters are created in such a way that the “radius” of each clusters is no more than the specified threshold.
::DEVELOPER
the Center for Bioinformatics and Computational Biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2011 Jun 30;12:271.
DNACLUST: accurate and efficient clustering of phylogenetic marker genes.
Ghodsi M, Liu B, Pop M.
:: DESCRIPTION
PClust is a scalable parallel software for detecting dense subgraphs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
C. Wu, A. Kalyanaraman.
An efficient parallel approach for identifying protein families in large-scale metagenomic data sets.
Proc. ACM/IEEE Supercomputing Conference (SC’08), Austin, TX, November 15-21. pp. 1-10. 2008
:: DESCRIPTION
AncestralClust is a clustering program, which is developed for clustering divergent sequences.
::DEVELOPER
Lenore Pipes @ Nielsen Berkeley Lab
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pipes L, Nielsen R.
AncestralClust: Clustering of Divergent Nucleotide Sequences by Ancestral Sequence Reconstruction using Phylogenetic Trees.
Bioinformatics. 2021 Oct 20:btab723. doi: 10.1093/bioinformatics/btab723. Epub ahead of print. PMID: 34668516.
:: DESCRIPTION
CFinder offers a fast and efficient method for clustering data represented by large graphs, such as genetic or social networks and microarray data. CFinder is a free software for finding overlapping dense groups of nodes in networks, based on the Clique Percolation Method, CPM, of Palla et. al. Nature (2005).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
CFinder: locating cliques and overlapping modules in biological networks.
Adamcsek B, Palla G, Farkas IJ, Derényi I, Vicsek T.
Bioinformatics. 2006 Apr 15;22(8):1021-3. Epub 2006 Feb 10.
:: DESCRIPTION
rKOMICS is an R package for processing mitochondrial minicircle assemblies in population-scale genome projects
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Geerts M, Schnaufer A, Van den Broeck F.
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects.
BMC Bioinformatics. 2021 Sep 28;22(1):468. doi: 10.1186/s12859-021-04384-1. PMID: 34583651; PMCID: PMC8479924.
:: DESCRIPTION
parastructure is a perl script collection to run the population genetics software STRUCTURE in parallel on a cluster (beowulf type).
::DEVELOPER
Jacques Lagnel (lagnel@her.hcmr.gr)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MarVis (Marker Visualization) is designed for intensity-based clustering and visualization of large sets of metabolomic markers.The application of 1D-SOMs gives a convenient overview on relevant profiles and groups of profiles. The specialized visualization effectively supports researchers in analyzing a large number of putative clusters, even though the true number of biologically meaningful groups is unknown. Although MarVis has been developed for the analysis of metabolomic data, the tool may be applied to gene expression data as well.
::DEVELOPER
Department of Bioinformatics , University of Göttingen
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kaever A, Lingner T, Feussner K, G?bel C, Feussner I, Meinicke P:
MarVis: a tool for clustering and visualization of metabolic biomarkers.
BMC Bioinformatics 2009, 10:92.
:: DESCRIPTION
CAFS (Clustering Analysis of Functional Shifts / Clusterfunc) is a simple and fast method for Clustering functionally divergent genes by Functional Category. The program analyses alignments and provides the user with the best putative sites under functional divergence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, et al. (2012)
Proteome-wide analysis of functional divergence reveals the molecular basis of ecological adaptations in bacteria .
PLoS ONE 7(4): e35659. doi:10.1371/journal.pone.0035659
:: DESCRIPTION
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Bison: bisulfite alignment on nodes of a cluster.
Ryan DP, Ehninger D.
BMC Bioinformatics. 2014 Oct 18;15:337. doi: 10.1186/1471-2105-15-337.
:: DESCRIPTION
Cluster 3.0 is an enhanced version of Cluster, which was originally developed by Michael Eisen while at Stanford University.
Cluster is program that provide a computational and graphical environment for analyzing data from DNA microarray experiments, or other genomic datasets. The program Cluster can organize and analyze the data in a number of different ways.
The main improvement consists of the k-means algorithm, which now includes multiple trials to find the best clustering solution. This is crucial for the k-means algorithm to be reliable.The routine for self-organizing maps was extended to include 2D rectangular geometries. The Euclidean distance and the city-block distance were added to the available measures of similarity.
::DEVELOPER
Michiel de Hoon of the University of Tokyo
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Reference: M. J. L. de Hoon, S. Imoto, J. Nolan, and S. Miyano:
Open Source Clustering Software.
Bioinformatics, 20 (9): 1453–1454 (2004).
