About the Phylap Applet

Version 0.1 Jan 1996. Version 0.2 Nov 2002.

The Phylap applet is used to demonstrate phylogenetic trees and their reconstruction. See the cover page and the pages referenced from it for its use.

The applet is written in Java. It can be viewed using Netscape 2.0. or later.

Phylap extends the Applet class. The following parameters may be passed to it.

species -- the number of extant species. Default 10.
chars -- the number of characters. Default 10.
alts -- number of alternatives per character. Default 4.
rate -- the mutation rate times 1000. Default 100.
method -- reconstruction method
- -1: minimum method
- 0: average method (default)
- +1: maximum method
showActual -- show actual tree
showGenome -- show genome sequences
showMatrix -- show distance matrix
showConstructed -- show constructed tree

Depending the the value of the layout parameter, various panels are inserted into the applet component. Some of these are control panels that can change some of the parameters or call for a new phylogenetic tree or request mutations. The panels are color coded. The actual phylogenetic tree and its controls are painted in one color, the distance matrix and the mutation controls are in another color, and the reconstructed phylogenetic tree and its controls are in a third color.

The phylogenetic trees are actually Phyltree objects, extensions of the Component class.

Source and object codes:

Plylap is the phylogeny applet. It forms the interface with the user. It reads the parameters from the html page and creates the window with various buttons, etc.

As far as the model goes, Phylap creates a random actual tree first with the instructions

Then it creates a distance matrix which depends on modelled mutations with the instruction

distanceMatrix = actualTree.mutationMatrix(chars,alts,rate); Finally it uses the distance matrix to reconstruct a tree with the instructions

In order to perform these three steps, first the random method of the Phyltree class is used to create a random tree. Then the mutationMatrix method of the Phyltree class is used to randomly create mutations along the tree. Finally the construct method of the Phyltree class is used to reconstuct a tree from the distance matrix.

Next page: web references.

Previous page: summary.

Table of contents: http://aleph0.clarku.edu/~djoyce/java/Phyltree.

David E. Joyce

Department of Mathematics and Computer Science
Clark University

January, 1996