Generation Information Of PTC

The Control Components of PTC

The Menu Layout of PTC


The Display Layout of PTC

Input Data

The input data allows users to type the data. When users open a file, the data is also shown in this area. The default number of species is 5, and the default number of sites in the character-based algorithm is 9. However, they can be changed from the Setting button, as we will describe later. Users must press any key when finishing typing the data in one cell. Otherwise, the data will not be accepted.

There are two different types of interface, the distance table and the character table. When users select different algorithms from the Algorithm menu, the interface changes accordingly. The default interface is the distance table.

Intermediate Results

In distance-based algorithms, the Intermediate Results show the new distance table when we join two nodes at each stage. In character-based algorithm (MP in the package), it shows the number of substitutions at each informative site, the total number of substitutions, and the characters for the interior nodes at each stage.

Instructions

The Instructions record the information about the construction of the tree at each step. Such information includes the minimum distance, the two nodes to be joined, and the branch length.

Phylogenetic Tree

The Phylogenetic Tree displays the phylogenetic tree. Leaf nodes are represented by squares in green color, while interior nodes are represented by dots in red color. Branch lengths are represented by blue lines with their lengths displayed above or under the lines.

In UPGMA and NJ, when the algorithm ends, the Phylogenetic Tree area displays the final tree. In FM and MP, separate windows, called Best Tree are used to hold the final best trees. In these cases, the Phylogenetic Tree area just displays the last tree in the algorithms.


Send comments and suggestions about PTC to khuri@cs.sjsu.edu or cherryyang@yahoo.com