User`s manual

Chapter 5: Analysis Tools
5-59
Distance Matrix
Select a method from the Distance Matrix pull down for calculating similarity. The
choices are Dice Coefficient, Jaccard Coefficient, Pearson Coefficient, and Frequency
Similarity. These are standard statistical algorithms, references can be found in most
statistical text books.
Cluster Method
Select a method for calculating the clustering from the Cluster Method pull down. The
choices are Neighbor Joining, UPGMA, WPGMA, Single Linkage, Complete Linkage,
Ward, Median, and Centroid. . These are standard statistical algorithms, references can
be found in most statistical text books.
Clusters
Select the number of clusters you would like displayed in the dendrogram. The values
are 1 to maximum number of lanes in the image. This option is disabled when Neighbor
Joining is chosen for the cluster method since the method determines the number of
clusters.
OutGroup
When Neighbor Joining is chosen for the cluster method the OutGroup option is enabled
allowing the user the ability to set the number of Out Groups to display.
Exporting and Printing the Dendrogram
Print and Export are selectable under the File menu. Select Print to send the report to a
local or network printer. Select Export to export the results to the clipboard or to file.
When exporting to a file there are two file types that can be saved, standard text file
(*.txt) or a comma separated value file (*.csv). When exporting to Excel, use the *.csv
file type to skip the Excel import wizard or use export to clipboard followed by Paste in
Excel.
Display Type
Under the View menu the user may select to view the dendrogram in the Phylogram or
Cladogram format.
Collapse/Expand
The Collapse/Expand tool allows the user to collapse or expand the dendrogram by
clicking on a red intersection marker.
Selection Tool
The selection tool allows the user to mouse out an area of interest within the dendrogram.
When the mouse is released you will be given the choice to Print, View, or Export the
selected region.