Ensemble NMF 0.91 / NMF Tree Browser 0.98 – Clustering and Visualising Protein Interaction Networks

DySC is a new tool based on the greedy clustering approach which uses a dynamic seeding strategy. Evaluations based on the normalized mutual information criterion shows that DySC produces higher quality clusters than UCLUST and CD-Hit at a comparable runtime.

::DEVELOPER

Zejun Zheng, Stefan Kramer and Bertil Schmidt

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

DySC

:: MORE INFORMATION

Citation

DySC: software for greedy clustering of 16S rRNA reads.
Zheng Z, Kramer S, Schmidt B.
Bioinformatics. 2012 Aug 15;28(16):2182-3. Epub 2012 Jun 23.

SLP – Single-Linkage Preclustering for improved OTU clustering

SLP

:: DESCRIPTION

SLP is a software for single-linkage preclustering for improved OTU clustering . It was based on pairwise distances this is used as a preliminary step before average linkage clustering of short (<250nt) sequences.

::DEVELOPER

The VAMPS project

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

SLP

:: MORE INFORMATION

Citation:

Huse, SM, Mark Welch, D, Morrison, HG, and Sogin, ML (2010)
Ironing out the wrinkles in the rare biosphere through improved OTU clustering.
Environmental Microbiology (2010) 12(7), 1889-1898.

GQL 1.0 – GHMM-based tool for Querying and Clustering Gene-Expression time-course data

GQL 1.0

:: DESCRIPTION

GQL (Graphical Query Language) is a suite of tools for analyizing time-course experiments. Currently, it is adapted to gene expression data. The two main tools are GQLQuery, for querying data sets, and GQLCluster, which provides a way for computing groupings based on a number of methods (model-based clustering using HMMs as cluster models and estimation of a mixture of HMMs).

::DEVELOPER

Alexander Schliep’s group for bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Tcl/Tk
GSL
Python
PyGSL

:: DOWNLOAD

GQL

:: MORE INFORMATION

Citation

Bioinformatics. 2005 May 15;21(10):2544-5. Epub 2005 Feb 8.
The Graphical Query Language: a tool for analysis of gene expression time-courses.
Costa IG, Schönhuth A, Schliep A.

CLUTO 2.1.2a / gCLUTO 1.0 – Software for Clustering High-Dimensional Datasets

CLUTO 2.1.2a / gCLUTO 1.0

:: DESCRIPTION

CLUTO is a software package for clustering low- and high-dimensional datasets and for analyzing the characteristics of the various clusters. CLUTO is well-suited for clustering data sets arising in many diverse application areas including information retrieval, customer purchasing transactions, web, GIS, science, and biology.

gCLUTO is a cross-platform graphical application for clustering low- and high-dimensional datasets and for analyzing the characteristics of the various clusters.

::DEVELOPER

Karypis Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows

:: DOWNLOAD

CLUTO / gCLUTO

:: MORE INFORMATION

Citation:

Matt Rasmussen and George Karypis.
gCLUTO: An Interactive Clustering, Visualization, and Analysis System.
UMN-CS TR-04-021, 2004.

COGRIM – Clustering of Genes into Regulons using Integrated Modeling

COGRIM

:: DESCRIPTION

COGRIM is an R program of Bayesian hierarchical model and Gibbs Sampling implementation that integrates gene expression, ChIP binding, and transcription factor motif data in a principled and robust fashion.

::DEVELOPER

the Computational Biology and Informatics Laboratory (in the Center for Bioinformatics at the University of Pennsylvania)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows
R Package

:: DOWNLOAD

COGRIM

:: MORE INFORMATION

Citation:

G. Chen, S. T. Jensen, C. Stoeckert,
“Clustering of Genes into Regulons using Integrated Modeling-COGRIM“,
Genome Biology, 2007, Jan. 4;8(1):R4

RNACluster 1.0 – RNA Secondary Structure Comparison and Clustering

RNACluster 1.0

:: DESCRIPTION

RNACluster is an integrated computational software which implements 6 common structure distances to measure the (dis)similarity of RNA secondary structures including base pair distance, mountain distance, morphological distance, tree edit distance, string edit distance and our in-house structure matrix distance, and one effective cluster approach for the ensemble clustering using a minimum spanning tree (MST) based algorithm. RNACluster can be used to study the characteristics of RNA secondary structures, RNA structure conformational switches, RNA conformational energy landscapes and RNA secondary structure prediction based on the clustering of structure ensemble.

::DEVELOPER

Qi Liu

:: REQUIREMENTS

Linux/Windows

:: DOWNLOAD

RNACluster

:: MORE INFORMATION

Citation

Liu Q, Olman V, Liu H, Ye X, Qiu S, Xu Y.
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
J Comput Chem. 2008 Jul 15;29(9):1517-26.

CompClust 1.2 – Explore and Quantify Relationships between Clustering Results

CompClust 1.2

:: DESCRIPTION

CompClust is a python package written using the pyMLX and IPlot APIs. It provides software tools to explore and quantify relationships between clustering results. Its development has been largely built around needs of microarray data analysis but could be easily used in other domains.

::DEVELOPER

the Wold Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsx/WIndows with Cygwin
Python
SciPy
NumPy
Pmw
BLT
TCL/TK

:: DOWNLOAD

CompClust

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2005 May 10;33(8):2580-94. Print 2005.
A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data.
Hart CE, Sharenbroich L, Bornstein BJ, Trout D, King B, Mjolsness E, Wold BJ.