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Phylogeny Clustering Analysis of DNA Fragment Data Automates Dendrogram Construction

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, Beckman-Coulter®, MegaBACE® genetic analyzers , with the Hierarchical Clustering method. 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.

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).

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).

Download Cluster Analysis Application Note (PDF)

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Research use only (RUO)

GeneMarker Applications:
Fragile X
MLPA® (Multiplex Ligation‐dependent Probe Amplification)
MS‐MLPA®
Trisomy Analysis
Macromolecule Analysis Tool
ARMs & Comparative Analysis (Cystic Fibrosis Analysis)
MSI (Microsatellite Instability) Analysis
Merge Project
Kinship Analysis of Wild Populations and data base
AFLP
t‐RFLP
Microsatellite (SSR, STR, VNTR)
MLVA
SBE/ SnapShot®
Cluster Analysis
TILLING® & EcoTilling with slabgel or capillary data
SNPWave®/SNPlex®
Haplotype Analysis
Loss of Heterozygosity Analysis (LOH)









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