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Applications

Software that can be categorized as ‘Applications’, i.e., not compilers, tools etc. For a full list see the A-Z list.

Bioinformatics

PACKAGE	NOTES
Augustus	Gene prediction tools
BART	(Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcription factors.
BayesTraits	Phylogeny analysis of trait evolution.
PBMPI	Bayesian phylogenetic reconstruction
BCFtools	Variant Call Format file manipulation tools
Bedops	A fast, flexible toolset for genome arithmetic.
Bedtools	A fast, flexible toolset for genome arithmetic.
BGEN (bgenix)	Tools to process genome data in BGEN format
Bioconductor (in R)	Tools for analysis and comprehension of high-throughput genomic data
BioPerl	Tools for analysis and comprehension of high-throughput genomic data
BLAST	Nucleotide or protein sequence matching statistics
BLAT	Protein alignment tool
Block	DMRG computational chemistry code
Bowtie	Sequence alignment
Bowtie2	Sequence alignment
BWA	Burrows-Wheeler Aligner, genome sequence mapper
corHMM	Evaluate models of binary character evolution
Cufflinks	Sequence assembly
EMIRGE	Ribosomal gene reconstruction python scripts
Ensembl Tools	Varient Effect Predictor script in perl
EVM	Gene processing
Fast-LMM	GWAS python tools for large datasets
FASTA Number	FAST processing scripts
FastQC	Sequence data quality control tool
fastStructure	Large SNP genotype data population inference
FSL	Library of analysis tools for FMRI, MRI and DTI brain imaging data
GATK	Genome Analysis Toolkit
GeneMark-ES	Gene prediction
Geneland	Statistical analysis of population genetics data in R
HiCUP	Genome mapping
HOMER	Software for motif discovery and next generation sequencing analysis
IDBA and IDBA-UD	Graph assemblers for second-generation sequencing reads
LDSC	Heritability and genetic correlation estimates
MACS	Model-based Analysis for ChIP-Seq
MACS2	Model-based Analysis for ChIP-Seq
Marge	Model-based Analysis of Regulation of Gene Expression
MaxBin	Binning assembled metagenomic sequences
MEGAHIT	Fast metagenomics assembly tool
metaVelvet	De novo metagenome assembly from short sequence reads
mmtsb toolset	Multiscale Modeling Tools for Structural Biology
MosaicFinder	Gene fusion identification tool
MrBayes	Bayesian Inference of Phylogeny
Picard	Tools for manipulating high-throughput sequence data
Primer3	Design PCR primers for genetics and molecular biology
Prodigal	Protein-coding gene prediction.
PySnpTools	SNP genome data python file processing
Quast and MetaQuast	Evaluation of genome assemblies.
QIIME	Comparison and analysis of microbial communities
RapMap	testing ground for ideas in lightweight / quasi / pseudo transcriptome alignment
RAxML	Maximum Likelihood based inference of large phylogenetic trees
Salmon	Fast transcript quantification from RNA-seq data
SAMtools	Sequence alignment and mapping tools
SCENIC	R workflow to process single-cell RNA-seq data.
Shellfish	Analysis of genome-wide SNP data
STACKS	Short-read sequence processing
Structure	Genetics software for investigating population structure
tabix	Generic indexer for TAB-delimited genome position files
TopHat	Splice junction mapper
Relion	Statistical Cryo-EM reconstruction
USEARCH	Sequence analysis
vcftools	Package for working with VCFfiles
Velvet	Genomic assembler
vsearch	Sequence analysis
Xaim	Graphical Molecule tool
X! Tandem	Mass spectra and peptide matching tool

Computational Chemistry, Molecular Dynamics

PACKAGE	NOTES
ADF	Amsterdam Density Functional computational chemistry
Amber	A general purpose molecular mechanics/dynamics suite
Autodock	Autodock4 and Vina – Molecular docking tools
CASTEP	Computational chemistry
CASTEPconv	Script to automate convergence calculations
CHARMM	A many-particle molecular simulation program
Chem Shell	Interactive shell for computational chemistry calculations
CRYSTAL	A general-purpose program for the ab-initio study of crystalline solids
DFTB+	Density Functional Tight Binding
DL_MESO	General purpose mesoscale simulation package. LBE and DPD.
DL_MONTE	Monte Carlo simulation of condensed phases.
DL_POLY	DL_POLY_CLASSIC, a general purpose classic MD suite
DL_POLY4	A general purpose classic MD suite
DynamO	Particle simulation and molecular dynamics
ELK	All-electron full-potential linearised augmented-plane wave code
Exciting	A full-potential linearised augmented-plane wave code
Gaussian	Performs semi-empirical and ab-initio molecular orbital calculations
GoodVibes	Quasi-harmonic thermochemical calculation from Gaussian files
Gold Suite	Protein Docking
GROMACS	GROMACS is a package for computing molecular dynamics of biochemical and non-biological systems
LAMMPS	Classical molecular dynamics code
Maestro	Molecular modeling tool
MDAnalysis	Molecular Dynamics trajectory analysis
MGLTools	Graphical molecular visualization tools.
MOE	Molecular Operating Environment
MOLCAS	Ab initio quantum chemistry software
MOLPRO	Ab initio quantum chemistry software
MOLDEN	Molecular Graphics Visualisation Tool
NAMD	Molecular Dynamics code
openbabel	Molecular data processing
openeye	A portfolio of molecular modeling applications for pharmaceutical research
Ovito	Scientific visualization and analysis of atomistic simulation data
ORCA	Ab initio, DFT and semiempirical SCF-MO package for quantum chemistry
Packmol	Initial configurations for Molecular Dynamics Simulations by packing optimization
pcazip	Trajectory compression tools
Phenix and Rosetta	Python-based Hierarchical ENvironment for Integrated Xtallography
Plumed	Free energy calculations in molecular systems
POLYRATE	Chemical reaction rates for polyatomics
PyCoCo	Process conformations within an ensemble of molecular structures using Python
pymol	Molecular visualization
PyPcaZip	Trajectory compression tools using Python
Quantum Espresso	Nanoscale materials modelling and electronic-structure calculations.
Towhee	Monte Carlo molecular simulation code
TURBOMOLE	Quantum chemistry – electronic structure calculations
VASP	VASP
Visual Colloids	Molecular visualization tool
VOTCA	Molecular Dynamics
VMD	Molecular Graphics Visualisation Tool

Computational Fluid Dynamics

PACKAGE	NOTES
ABAQUS	Finite Element Analysis
ACE	Computational Fluid Dynamics
CFX	Computational Fluid Dynamics
Code Aster	Finite Element Analysis for structural and civil engineering
Code Saturne	General Purpose Computational Fluid Dynamics Software
DynamO	Particle simulation and molecular dynamics
FDS	Fire Dynamics Simulator
Fluent	A computational fluid dynamics package
Gerris2D / 3D	Fluid flow solver
gpyro	Generalized Pyrolysis Model for Combustible Solids
OpenFOAM	Fluid dynamics platform
PowerFLOW	Fluid flow simulation
StarCCM+	A computation continuum mechanics application
Star-CD	Computational fluid dynamics simulation
Telemac	Free-surface flow solvers

Finite Element Modelling

PACKAGE	NOTES
ABAQUS	Finite Element Analysis
LS-DYNA	A general purpose explicit solver
Materials Studio	Materials modeling and simulation
MUMPS	MUltifrontal Massively Parallel sparse direct Solver on AMD Bulldozer compute nodes
Yade	C++/Python DEM framework

Mathematics

PACKAGE	NOTES
FICO Xpress	Optimization and data analytics tools
Mathematica	Numeric and symbolic computing and programming
MATLAB	Numerical computation, visualization and programming.
Octave (GNU)	Free MATLAB-like application for numerical calculations
PyGMO	Parallel optimization framework in python
R	Statistical computing and graphics. Includes bioconductor.
RStudio	GUI-based development environment for R
Stata	Data analysis and statistical software

Multiphysics and Solvers

PACKAGE	NOTES
ANSWERS	A suite of monte-carlo nuclear simulation tools
LS-DYNA	A general purpose explicit solver
Elmer	multiphysical simulation
Materials Studio	Materials modeling and simulation
PyGMO	Parallel optimization framework in python
Serpent	Monte-carlo Nuclear reactor physics
StarCCM+	A computation continuum mechanics application
WRF (and WPS)	WRF weather research and forecasting model
WRF-Chem	Weather Research and Forecasting (WRF) model coupled with Chemistry
Yade	C++/Python DEM framework

Neural Networks and Machine Learning

PACKAGE	NOTES
Chainer	Neural netowrks in python
Keras	Neural Network python API using Tensorflow
LENS	Neural Network Simulator
TensorFlow	Data flow graph processing
Theano	Multi-dimensional array processing

Visualization

PACKAGE	NOTES
EMAN2	Greyscale scientific image processing
ffmpeg	Image processing
Freesurfer	Visualisation of structural and functional brain imaging data
FSL	Analysis of structural and functional brain imaging data
Gephi	Graph visualization and analysis
IDL	Data visualization programming language
MGLTools	Graphical molecular visualization tools.
Ovito	Scientific visualization and analysis of atomistic simulation data
Povray	Raytracer for rendering 3D models
ParaView	Scientific Visualization application based on VTK
Visual Colloids	Molecular visualization tool
VMD	Molecular Graphics Visualisation Tool
XCrySDen	Molecular visualisation tool

Last modified on August 1, 2018 at 5:08 pm by George Leaver

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