- HybridInterleave, a Java program for an exact calculation of the minimum number of hybridization events to explain two rooted binary phylogenetic trees on the same taxa set.
- Collins, J., Linz, S., and Semple, C. Quantifying hybridization in realistic time. Journal of Computational Biology, in press.
- AncestralBuild, 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. Systematic Biology 55 (2006), 270-288.