Creating a Minimum Spanning Tree based on MLST data
This tutorial illustrates how to create a Minimum Spanning Tree (MST) based on MLST allele numbers. The same steps are also applicable for clustering of other categorical character data sets such as MLVA.
Characters
A character is basically a name-value pair of which the value can be binary, multi-state or continuous. Because of this very broad definition, a wide variety of data can be analyzed as character types (= an array of characters). This includes morphological and biochemical features, commercial test panels (API®, Biolog®, Vitek®, etc.), antibiotics resistance profiles, fatty acid profiles, microarrays, SNP arrays, repeat numbers in MLVA, allelic profiles in MLST, etc.
Demonstration database containing 500 Neisseria strains with sequences and allele IDs for the seven housekeeping genes, present the publicly available MLST scheme hosted at www.pubmlst.org.
Note that the downloaded database backup file (.bnbk) can be restored via the Restore database... functionality in the BIONUMERICS startup screen.