Tree viewing

TreeView and TreeView X

View NEXUS, PHYLIP, Clustal, Hennig86, etc. format tree files on Macs (68K and Power Mac) and Windows (16 and 32 bit). Unix version as well (TreeView X).

Data entry

NDE

NDE (NEXUS Data Editor) is a program to create and edit NEXUS format data files on computers running Microsoft Windows 95/NT 4.0. The main motivation behind my writing the program was to provide an easy to use data editor similar to that provided in the Macintosh program MacClade (note that NDE has none of the data or tree analysis features of MacClade).

Tree building

GeneTree

GeneTree is an experimental program for comparing gene and species trees using reconciled trees.

Spectrum

Finds bipartition spectra of molecular data (Macintosh and Windows95/NT).

Tree comparison

COMPONENT

COMPONENT is a computer program for analysing evolutionary trees and is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography. Originally for Windows, a preliminary Mac version was written in 1997, and the source code for the Windows verison is now available.

RadCon

RadCon is a free phylogenetic tree consensus and comparison program, for the MacOS, written by Joseph L. Thorley and Roderic D.M. Page. Features of note include the strict reduced consensus method, leaf stability, cladistic information content, double decay analysis and matrix representation with parsimony.

TreeMap

Software for comparing host and parasite phylogenies (Windows and Macintosh).

RNA secondary structure

Circles

A program to automate the inference of RNA secondary structure using the comparative method