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.

Download PDF file: 
PDF icon MST_MLST_data.pdf
Download sample data: 
Neisseria MLST data
MS Excel file, containing MLST allelic profiles for 500 Neisseria meningitidis strains, including serogroup and strain information.
Download demonstration database: 
Neisseria MLST demo database

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.