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.
List of the main numerical simulation applications and visualization tools available on the clusters./p>
- The Pencil-Code- is a high-order finite-difference code for compressible hydrodynamic flows with magnetic fields. Click here for more information.
- The Rames Code (Adaptive Mesh Refinement) method used for general purpose simulations in self-gravitating fluid dynamics. The code is free software written in Fortran 90 with extensive use of the MPI library. Click here for more information.
- IDL - data analysis, data visualization. This is a licensed software package.