software

Bioinformatics Software
Amber		Assisted Model Building with energy refinement. Used for biological and molecular simulations.
ATLAS		Provides optimal software for lineal algebra.
BLAS		Routines for operations with vector and matrices.
EasyBuild		Framework for installing software
GAMESS		General Atomic and Molecular Electronic Structure System, a general ab initio quantum chemistry package.
gamos5		Geant4-based medicine-oriented-simulations. gamos5 simulates of the passage of particles through matter.Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
Gaussian		Provides state-of-the-art capabilities for structure modeling.
gcc, g++, gfortran		Compilers and its libraries.
gnuplot		Gnuplot is a command-line driven graphing utility used to visualize mathematical functions and data interactively.
GSL
Lapack		Routines for solving lineal equations, eigenvalue problems.
Ligplot		Program for automatically ploting protein-ligand interactions.
Matlab		A programming language that allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces and interfacing with programs written in other languages.
MPICH		High performance and widely portable implementation of MPI.
Octave		High-level interpreter language for numerical computations. It provides capabilities for numerical solution of lineal and nonlineal problems, and graphic capabilities for data manipulation and visualization.
OpenMPI		Open source Message Passing Interface (MPI) implementation.
pgapack		Parallel Genetic Algorithm Library
python		A widely used high-level, general-purpose, interpreted, dynamic programming language.
R		Free software environment for statistical computing and graphics.
Scilab		Opensource software for numerical computations.
Weka		Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization.
MrBayes		MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
BEAST		BEAST2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
RAxML		RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for post- analyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.