Biological applications of data clustering calculations include phylogeny analysis and community comparisons in ecology, gene expression pattern, enzymatic pathway mapping, and functional gene family classification in the bioinformatics field. It has been successfully paired with the AFLP, microsatellite and RAPD analysis techniques for a variety of applications.
GeneMarker software combines accurate genotyping of raw data from ABI®PRISM, Applied Biosystems SeqStudio™, and Promega Spectrum Compact CE genetic analyzers and custom primers or commercially available chemistries with Hierarchical Clustering analysis methods. The program treats each data point as a single cluster and successively merges clusters until all points have been merged into a single remaining cluster. Researchers may select from different linkage types - Single, Complete or the Average - for the clustering algorithm. Results are presented as a dendrogram and a table providing Euclidian distances between each point.
Figure 1: Dendrogram from Cluster Analysis of 30 files using allele calls from one multiplex (left) and dendrogram of the same files based on the combined results of 3 multiplexes (right).
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