UZ | University of Zimbabwe

ITEM	APPLICATION	USAGE	APPLICATION AREAS
1	MATLAB	Use for algorism development, data visualization, data analysis and senior technology computing language and interactive environment of numerical calculation	Math and computation, Algorithm development. Modeling, simulation, and prototyping, Data analysis, exploration, and visualization, Scientific and engineering graphics, Application development, including Graphical User Interface building.
2	Mathematica	One set of scientific computing software which combines numeric and symbolic calculation engine, graphic system, programing language and text system.	Comprehensive Image Processing Environment, Graphs and Networks Modeling, Graphs and Networks Analysis’, Integrated Control Systems Design, Integrated Wavelet Analysis, Built-in Financial Computations, Import and Export Formats
3	Red Hat linux	Operating system
4	Discovery Studio	New molecular modeling environment, professional life science molecular simulation software	Molecular Mechanics, Molecular Dynamics, Quantum Mechanics, Simulations, Ligand Design, Macromolecule design and validation, Macromolecule engineering
5	Dock	Molecular docking software	Bi0-infomatics, Drug Discovery
6	Autodock	Molecular couple rings software package	Structure-based Design, Lead Optimization, Virtual Screening, protein-protein docking, chemical mechanism, Drug Discovery, Bio-informatics
7	Modeller	Isogeny or comparative protein three dimensional structure modeling software	Bio-informatics
8	BWA	Sequencing adjustment read software of large reference genome	Computational Chemistry
9	BLAST	Protein database or DNA database similarity comparison and analysis tool	Bioinformatics,
10	MPIBLAST	Parallel sequence alignment software
11	FASTA	Database similarity searching program	Bioinformatics
12	Velvet	Short sequence assembly tool. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.	Bioinformatics
13	Gromacs	Molecular dynamics general software package, imitate particles system Newton motion formula	Computational chemistry research
14	NAMD	Simulate parallel molecule dynamics code of macromolecule system, and calculate atom track. NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. Simulation preparation and analysis is integrated into the visualization package.	molecular dynamics simulation-computational chemistry
15	CHARMM	Molecule dynamics software, conduct classical, quantum or quantum classical hybridization simulation. A molecular simulation program with broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques including QM/MM, MM/CG, and a range of implicit solvent models. ► CHARMM primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM also finds broad applications for inorganic materials with applications in materials design.	Bioinformatics and computational chemistry
16	LAMMPS	Large-scale atomic and molecular parallel simulator. has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.	Engineering, electrical and mechanical usage
17	VMD	Molecule visualization program, apply 3D graphic and built-in script to display large-scale molecular system, animation production and analysis.	Molecule visualization in computational chemistry and bioinformatics
18	ARP/wARP	Macromolecular modeling software.It is macromolecular model automatically, with a reproducible computational procedure	Structural genomics, X-ray crystallography, software, model building, ligand placement
19	Cns	Macromolecular structure research software	Computational Chemistry
20	X!tandem	Proteomics database retrieval software	Protein identification.
22	EMAN	Single particle refactoring software	Structural Analysis
23	IDL	Data analysis and graphic application program and programing language, which can transform data into graphics, and enhance analysis and understanding	Statistical Analysis
24	Tecplot	Visualization software, to map and generate animation based on data and conduct analysis on complicated data, make multiple layout arrangement, and form relevance of outcome, graphics and animation.	Computational Fluid Dynamics
25	Origin	Graphics visualization and data analysis software is a common senior data analysis and mapping tool by scientific researchers and engineers.	Scientific Graphing
26	WRF	Weather research and forecast system model	Weather Forecasting and Climate Modelling
27	MM5	Mesoscale numerical forecast model	Weather Forecasting and Climate Modelling
28	CCSM	Unifying weather system model. It is a complete coupling model research system combines atmosphere, ocean, land and sea ice.	Weather Forecasting and Climate Modelling
29	Gaussian	Quantum chemistry software package, forecast period system energy, structure and molecular track.	Computational Chemistry
30	Dacapo	Java benchmark test tool	Computational Chemistry
31	Abinit	Based on density functional theory, apply pseudo potential and plane wave vector method to deal with electron and nuclear constituting system.	Computational Chemistry; Materials Science
32	CPMD	First principle molecular dynamics method, which applies pseudo potential, plain wave basic vector and density functional theory (DFT), calculates applied force between atoms (molecules).	Computational Chemistry; Molecular Dynamics
33	Materials Studio	Simulating software of material science field. Convenient to set up three-dimensional structure model, target on all crystals, amorphous and macromolecular material quality and related process.	Computational Chemistry; Materials Science
34	VASP	Apply pseudo potential and plain wave basic vector. Software package to conduct calculation from quantum dynamics and molecular dynamics.	Computational Chemistry; Molecular Dynamics
35	WIEN2K	Apply density functional theory to calculate electronic structure of solid.	Computational Chemistry
36	TURBOMOLE	Quantum chemistry computing software, rapidly and stably deal with industrial application molecule.	Computational Chemistry; Quantum Chemistry
37	Siesta	Use for simulation of molecule and solid electronic structure calculation and molecular dynamics.	Computational Chemistry; Molecular Dynamics; Materials Science
38	Ansys	Large-scale general software of finite element analysis that integrates structure, fluid, electric field and sound field analysis.	Computational Chemistry; Engineering Simulation
39	CFX	General computing dynamics software based on partition structuring and control volume method.	Computational Chemistry; Computational Fluid Dynamics
40	Fluent	Fluid dynamics software	Computational Fluid Dynamics ; Computational Chemistry
41	FDS	Fluid dynamics calculation model, emphasize on smoke flow and thermal transmission study.	Computational Chemistry; Materials Science
42	Phaser	General simulating toll for dynamic system, suit for graph and numeric simulation analysis of difference/difference equation.	Statistical analysis
43	Shirondiger Suite	Chemical simulation software for use in pharmaceutical, biotechnology, and materials research.	Computational chemistry – Drug discovery
44	Pymol	Stunning high-performance molecular graphics for communicating structural results	Bioinformatics -DNA analysis
45	Chimera	Highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps,	Bioinformatics -DNA analysis
46	Jmodeltest	A Java-enabled application that can help scientists to analyze nucleotide substitutions, with up to five model. Application that can perform a selection of nucleotide substitutions, useful in DNA analysis, with support for large packets of data.	Bioinformatics -DNA analysis
47	Figtree	FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.	Bioinformatics
48	Sparks	Engine for large-scale data processing that performs in-memory computing. Spark offers bindings in Java, Scala, Python and R for building parallel applications.	Statistical Analysis
49	Phyml	Phyml estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. Phyml offers a large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches.	Bioinformatics
50	DataWarrior	Cheminformatics Program for Data Visualization and Analysis. DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence	Computational chemistry
51	FreeFem++	Allows the resolution of partial differential equation using the finite element method.	Statistical Analysis