Gaussian is a very popular general purpose electronic structure program. Recent versions can perform density functional theory, Hartree-Fock, Möller-Plesset, coupled-cluster, and configuration interaction calculations among others. Geometry optimizations, vibrational frequencies, magnetic properties, and solution modeling are available. It performs well as black-box software on closed-shell ground state systems.
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
The following versions of bedtools are available on OSC clusters:
Gurobi is a mathematical optimization solver that supports a variety of programming and modeling languages.
The following versions of bedtools are available on OSC clusters:
LS-OPT is a package for design optimization, system identification, and probabilistic analysis with an interface to LS-DYNA.
The following versions of ls-opt are available on OSC clusters:
Clustal W is a multiple sequence alignment program written in C++.
The following versions of bedtools are available on OSC clusters:
MUSCLE is a program for creating multiple alignments of protein sequences.
The following versions of bedtools are available on OSC clusters:
metilene is a software tool to annotate differentally methylated regions and differentially methylated CpG sites.
The following versions of bedtools are available on OSC clusters:
PyTorch is an open source machine learning framework with GPU acceleration and deep neural networks that is based on the automatic differentiation in the Torch library of tensors.
CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods and classical force fields.
ORCA is an ab initio quantum chemistry program package that contains modern electronic structure methods including density functional theory, many-body perturbation, coupled cluster, multireference methods, and semi-empirical quantum chemistry methods. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties. ORCA is developed in the research group of Frank Neese. Visit ORCA Forum for additional information.
