MicroStation System, MicroLog Version 4.2 - DTU Systems Biology ...

Data Management and Compiling Databases
Cluster Analysis
Cluster analysis uses a mathematical approach to display the relative
similarities and differences between strains or species based on pattern
matching. It offers a visual method for examining groups using linear
dendrograms and two- and three-dimensional cluster diagrams. You
can generate cluster analyses on groups of entries in Biolog’s database
or your own database.
The math behind cluster analysis
Dendrograms are generated using a modified UPGMA analysis
developed by Biolog (algorithm for constructing rooted phylogenic
trees). The algorithm uses DIST values to generate the branching
structure of the dendrogram. A DIST value of 14 is usually used as a
cutting level to separate genera. This value has been empirically
determined to be an appropriate one for most genera of gram-negative
bacteria.
Once the software generates a preliminary dendrogram, it makes a
second pass, rotating all branch points to their most preferred position.
This best maintains proximity of related strains or species. If the
distance between strains or species adjacent to cut points is less than
14, they are joined with a dashed line that indicates their actual
distance.
By mathematically removing the linear constraints of the dendrogram,
the software can generate two- and three-dimensional diagrams of
DIST relationships.
All of these cluster diagrams are only approximations of true
relationships. With 95 carbon source tests, it would take 95dimensional
space to provide fully detailed clustering. As a practical
matter, the linear dendrograms and two- and three-dimensional
diagrams give very satisfactory representations.
Using cluster analysis with IDs
1. Once you get a species ID, click the Cluster Menu selection bar on
the Data window.
MicroStation System/MicroLog User Guide Apr 07 Section 7 � Page 23