A phylogenetic tree visualization, analysis and comparison software.
Shiming Dong, Email: dong@cs.uga.edu , Computer Science Department, The University of Georgia.
Description
TreeAnalyzer is a phylogenetic tree visualization and analysis software package. TreeAnalyzer reads a phylogenetic tree from a PAUP NEXUS or TreeAnalyzer format file and visualizes it in a tree structure. The MAST metric is used in TreeAnalyzer to compare multiple trees and the resultant MASTs are visualized by mapping them onto the original compared trees. A normalized number is computed to represent the proportion of common parts of those trees. The compared trees may have different numbers of leaves or different leaf names. Theoretically, there is no limitation on the number of trees compared and the number of leaves they have. In practice, good performance has been observed for sample trees of real data with fewer than 100 leaves. In practice, the target users typically deal with trees containing up to 50 to 100 leaves. Users may interact with the visualized phylogenetic trees and the created MASTs to perform manipulations such as modifying leaf names, swapping the subtrees of a specific internal node, or changing the font of leaf labels. This software is developed using Java (J2sdk1.4.1) and runs on any platform that supports Java.
Download
Java source code are provided in TreeAnalyzer.zip
Two sample input files "Salmonella3repprimersNEXUS.txt" and "SalmonellaRiboprintNEXUS.txt" are contained in the package as a test.