Research in Comparative Biology and Genomics use several bioinformatics software applications from the public-domain and home-grown applications.
- POY (Phylogenetic Analysis of DNA and other Data using Dynamic Homology)-estimates phylogenies and alignments of using maximum parsimony or maximum likelihood optimality criteria.
- Malign- is a multiple alignment procedures that operates on close parallels to those used to search for minimum length cladograms.
- RaxML- is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. RAxML offers two ways to exploit parallelism: fine-grained parallelism that can be exploited on shared memory machines or multi-core architectures and coarse-grained parallelism that can be exploited on Linux clusters.
- MrBayes - is a free software program that employs Bayesian estimation of phylogeny. Click here for more reference information.