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Applications

Bioinformatics

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.

Astrophysics-MHD

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.

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