Help Menu for PhyloTree Display

• Introduction

  The Phylogenetic Tree Display provides a graphic overview of genetic diversity data for cotton. It is composed of internal/leaf nodes, the leaf nodes representing genotypes and the internal nodes allow the selection of sub-trees with a mouse click.

  1. Complete Tree display
  2. Subtree display
  3. Toggle between long and short leaf nodes
  4. Select coefficient cutting line
  5. A note on overlapping nodes
  
  
  

• Complete Tree display

  This display allows users to view the entire tree, select sub-trees and generate diversity clusters by moving the cutting line with a mouse click over the horizontal scale.
  
  
  

• Subtree Display

  A mouse click on any of the internal nodes will launch a view of the sub-tree that is rooted on the selected node.
  
  
  

• Toggle between long and short leaf nodes

  The leaf nodes can be displayed in two ways: short and long. With the option of short view, each node is drawn based on its height and length while long view aligns all leaf nodes to the right. The two views can be switched by clicking on the corresponding buttons on the top of the display.

  
  
  

• Select coefficient cutting line

  The coefficient cutting line indicates the user selectible position that differentiates groups/clusters of genotypes. Its value is selected by a mouse click over the horizontal bar on the top of the display. Clusters are indicated by color and leaf nodes that are located to the left of the cutting line are colored gray.

  
  
  

• A note on overlapping nodes

  This figure shows a situation where two nodes overlay. It occures when one node has a length of zero.