A 3D viewer for phylogenetic trees. Speciation events are displayed in the plane according to the species tree, while duplication events are displayed in the other dimension.
The TREEFINDER application computes phylogenetic trees from molecular sequences. The program infers even large trees by maximum likelihood under a variety of models of sequence evolution. It accepts both nucleotide and amino acid data and takes rate heterogeneity into account. Separate models...
TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It has a subset of the functionality of the...
IGRAFU is an open source program to integrate solutions to rebuild phylogenetic trees. It supports various well-known algorithms, such as Maximum Parsimony and Distance-matrix methods.
JPhylo is a Java based visualization program used to display sequences of phylogenetic trees.
PhyloPattern is a Java/Prolog API, helpful to simulate human reading of phylogenetic trees. Bioinformatician can: annotate trees, apply complex patterns to a tree to search specific architectures or extract information, compare trees with dynamically gen
PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
Phyloview is a perl based CGI script for visualizing taxonomic properties of protein phylogenetic trees.
TopiaryExplorer is developed in the Knight Lab at the University of Colorado at Boulder with the initial goals of supporting visualization of large phylogenetic trees and associated tip metadata and environmental data.TopiaryExplorer supports visualization of very large trees (it has been tested...
TreeViewJ is a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches, and add names to nodes. Collection dates can be mapped onto a timeline, and sorted.