Software
From SNIC Documentation
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 | ||
