Software

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This page lists software in use at various SNIC centres. Note that the centres can in most cases install additional software if there is need for it, and if so, please contact centre support directly through the standard support channels.

Field Description
ABINIT Computational materials science
Computational chemistry
density-functional theory code
ABySS Bioinformatics A parallel assembler for short read sequence data
ACML System tool
Numerical library
efficient mathematics library
ANFO Bioinformatics A parallel assembler for short read sequence data
ANNOVAR Bioinformatics Functional annotation of genetic variants from high-throughput sequencing data
ANSYS Computational fluid dynamics large modeling suite
ARC client Grid computing
Swestore
tool for accessing the Grid resources
ASE Computational materials science framework for setting up and analyzing atomistic simulations
Ab wtp Bioinformatics Alignment tool for SOLiD transcript reads
Abaqus Solid mechanics finite-element package
Amber Computational chemistry
Molecular dynamics
molecular dynamics
BEDTools Bioinformatics BEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format
BLAST Bioinformatics package for aligning nucleotide or amino acid sequences
BLAT Bioinformatics an alignment tool like BLAST, but it is structured differently.
BWA Bioinformatics A fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target).
BclConverter Bioinformatics Converts bcl files to Qseq files.
BioPerl Bioinformatics A community effort to produce Perl code which is useful in biology.
BioPython Bioinformatics A set of freely available tools for biological computation written in Python by an international team of developers.
Bioscope Bioinformatics the pipeline stack that comes with the solid sequence platform
Bowtie Bioinformatics Bowtie is an ultrafast, memory-efficient short read aligner.
CASAVA Bioinformatics Illumina's Consensus Assessment of Sequence and Variation (CASAVA) software
CASTEP Computational materials science
Computational chemistry
electronic structure calculation
CDO Climate research data analysis
CESM1 Climate research global climate model
CP2K Computational materials science
Computational chemistry
atomistic and molecular simulations code
CPMD Computational materials science
Computational chemistry
plane-wave DFT
CS-Rosetta Bioinformatics de novo protein structure generation
CSA Bioinformatics Python implementation of the Connection-set Algebra (Djurfeldt 2012)
Ccp4 Structural biology
Visualisation
determining macromolecular structures by X-ray crystallography
Charmm Computational chemistry atomistic and molecular simulations code
ClustalW Bioinformatics popular multiple sequence aligner
Comsol Computational materials science
Computational fluid dynamics
Commercial Mulitphysics Similation software
Concaterpillar Bioinformatics A hierarchical likelihood ratio test for phylogenetic congruence.
Coot Structural biology
Visualisation
software for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data
Cufflinks Bioinformatics Assembles transcripts in RNA-Seq samples and calculates their abundances
Cyana Bioinformatics
Structural biology
biological macromolecule structure calculation based on NMR conformational constraints
DDT System tool Debugger
DIANA Solid mechanics commercial FEM package
Dacapo Computational materials science
Computational chemistry
plane-wave DFT
Dalton Computational chemistry powerful molecular electronic structure program.
Desmond Molecular dynamics
Computational chemistry
molecular dynamics package
EC-Earth Climate research global climate model
EMBOSS Bioinformatics A free Open Source software analysis package developed for the molecular biology.
EMMAX Bioinformatics A statistical test for large scale human or model organism association mapping accounting for the sample structure.
EMTO Computational materials science Exact Muffin-Tin Orbitals method, an electronic structure code based on the Green's function technique
EMTOx Computational materials science Exact Muffin-Tin Orbitals method (x), an electronic structure code based on the Green's function technique
ESPResSo Computational materials science
Computational chemistry
molecular dynamics of soft matter systems
Edge Computational fluid dynamics unstructured CFD solver
Efield Computational electromagnetics simulation environment for electromagnetic simulations
Elk Computational materials science
Computational chemistry
all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features
… further results


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