Software and Algorithms
- Code for maxRAF algorithm
- RAF-Analyser - a web application for analysing Reflexively Autocatalytic Food-generated sets.
- HybridNumber (ZIP, 119 KB), a Perl script for an exact calculation of the minimum number of hybridization events to explain two rooted binary phylogenetic trees on the same taxa set.
- Bordewich, M., Linz, S., St. John, K., and Semple, C. A reduction algorithm for computing the hybridization number of two trees (PDF, 173 KB). Evolutionary Bioinformatics 3 (2007), 86-98.
- AncestralBuild (TAR.GZ, 1.75 MB), a Java programme for deciding if a collection of phylogenies with nested taxa is compatible.
- Berry, V. and Semple, C. Fast computation of supertrees for compatible phylogenies with nested taxa (PDF, 345 KB). Systematic Biology 55 (2006), 270-288.
- sim_tree (TAR, 190 KB) - Does Random Tree Puzzle produce Yule-Harding trees in the many-taxon limit? (Sha Zhu and Mike Steel, Mathematical Biosciences). This software is used to simulate tree topologies under the Yule process and the PDA process.
Index Of Patchiness for Stations
Algorithm by Dr. Jennifer Brown. Programming by Dietrich Radel
Windows executable version. (ZIP, 171 KB)
C source code in a .tar.gz file (TAR.GZ, 4 KB)
C source code in a .zip file (ZIP, 5 KB)
Contact Jennifer Brown, for help.
Algorithm for Trap Catch Index of Patchiness
Brown, J.A., McAuliffe, R.J. and Hickling, G.J. A new trap-catch index of patchiness in animal distribution. Submitted to Wildlife Research, 2nd revision April 2004.
The Annual New Zealand Phylogenetics Meeting
Download the most recent Phylogenetics Meeting photo collage (PDF, 1.62 MB) of snaps taken over the first 20 years of meetings.
Tuatara: Conservation priority in a phylogenetic context
Tuatara package for Mesquite - by Wayne P. Maddison & Arne Ø. Mooers.
Download the package from the mesquiteproject.org website.
Cited Papers
- Ancestral state reconstruction: 2011 BSc Honours project by Thomas (Heyang) Li
Misc
- A brief comparison of figure generation methods for LaTeX documents (PDF, 72 KB)
- Marcel Dekker's thesis (PDF, 21 MB)
