Pajek Clustering

This function takes clustering data and plots it, if the data is 2d or 3d. The inputs are:An m-by-d matrix of data points, where d is the number of dimension and m the number of data pointsAn m-by-1 vector of indices that associate each data point with a cluster.Optional inputs:A c-by-d matrix... Platforms: Matlab

Algorithm StrAP, is able to adaptively cluster data streams with Affinity Propagation. Several steps are made to buildStrAP. The first one (Weighted AP) extends AP to weighted items withno loss of generality. The second one (Hierarchical WAP) is concernedwith reducing the quadratic AP complexity,... Platforms: Matlab

WCluster is a java program designed to perform hierarchical clustering. Whereas most hierarchical clustering software only allows users to assign weights to either rows or columns, WCluster lets you assign weights to individual data points. For example, this can be very useful if a particular row... Platforms: Mac

As recently published in Science (see reference)Simple and effective means of clustering any data for which a similarity matrix can be constructed. Does not require similarity matrix meet the standards for a metric. The algorithm applies in cases where the similarity matrix is not symmetric (the... Platforms: Matlab

JUDGE (Java Utility for Document Genre Eduction) features automatic classification and clustering of documents, optionally as a webservice.The program is written entirely in Java and makes use of the Weka machine learning toolkit. Platforms: Windows, Mac, Linux

MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic Platforms: Windows, Mac, Linux

Scarlet is an extension for Atlassian JIRA, the leading Enterprise issue tracking and management software, allowing easy clustering of JIRA application instances, ensuring both high availability and linear scalability. Platforms: Windows, Mac, Linux

The FindCore Toolbox (v. 1.0b)David Snyder and Gaetano Montelione, (C) 2010This Matlab Toolbox implements the FindCore algorithm described in Snyder, D.A.; Montelione, G.T. PROTEINS: Struct. Funct. Bioinformaticsm, 2005, 59: 673-86. Clustering algorithms for identifying core atom sets and for... Platforms: Matlab

Codes for fuzzy k means clustering, including k means with extragrades, Gustafson Kessel algorithm, fuzzy linear discriminant analysis. Performance measure is also calculated. Platforms: Matlab

Many ant species exhibit the behavior of clustering corpses to form cemeteries. Each ant seems to behave individually, moving randomly in space while picking up or depositing (dropping) corpses. The decision to pick up or drop a corpse is based on local information of the antd-deOaos current... Platforms: Matlab

This is a tool for K-means clustering. After trying several different ways to program, I got the conclusion that using simple loops to perform distance calculation and comparison is most efficient and accurate because of the JIT acceleration in MATLAB.The code is very simple and well documented,... Platforms: Matlab

Measure percentage of Accuracy and the Rand index of clustering resultsThe number of class must equal to the number clusterOutput Acc = Accuracy of clustering results rand_index = Rand's Index, measure an agreement of the clustering results match = 2xk matrix which are the best match of the... Platforms: Matlab

The code for the spectral graph clustering concepts presented in the following papers is implemented for tutorial purpose:1. Ng, A., Jordan, M., and Weiss, Y. (2002). On spectral clustering: analysis and an algorithm. In T. Dietterich, S. Becker, and Z. Ghahramani (Eds.), Advances in Neural... Platforms: Matlab

Nowadays due to the yearly multiplying data comes always the claim for useful methods and algorithms that make the processing of these data easier. For the solution of this problem data mining tools come into existence, to which the clustering algorithms belong. At the Department of Process... Platforms: Matlab

brCluster is a class library, written in java, that implements generic clustering algorithms carefully designed to allow its aplication in any kind of data. The algorithms implemented are K-means and Hierarchical Clustering (Simple and Complete Link). Platforms: Windows, Mac, Linux

KlustaKwik is an open-source C++ and Java program for automatic clustering of continuous data into a mixture of Gaussians. The program was originally developed for sorting of neuronal action potentials, but can be applied to any sort of data. NOTE (25/04/12): For those interested in trying the... Platforms: Windows, Mac, BSD, Linux

PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains. Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to... Platforms: Mac, Linux

This user interface allows a user to load some Affymetrix data in an Excel file and perform some basic operations on it - log transform, log ratio, normalization, noise reduction, filtering, PCA and clustering, in addition to some visualizations like profile plots, boxplots and matrix... Platforms: Matlab

(SE) is developed to estimate the number of clusters (NC) for PAM clustering algorithm. By inspecting whether it is stable that two potential clusters are separated or merged, SE focuses on the separability of two closest clusters among k potential clusters (called twin-clusters) when a data set... Platforms: Matlab

The statistics toolbox contains routines for hierarchical clustering, including the cluster routine uses the SAHN tree to group data into clusters. However, the toolbox seems to lack a routine that uses the SAHN tree to describe the hierarchical relationship between those clusters. This routine... Platforms: Matlab