Software

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This page lists software in use at various SNIC centres.

 Research areaLicenseDescription
ABINITFreedensity-functional theory code
ABySSFreeA parallel assembler for short read sequence data
ACMLRequires licenseefficient mathematics library
ANFOFreeA parallel assembler for short read sequence data
ANNOVARFreeFunctional annotation of genetic variants from high-throughput sequencing data
ANSYSRequires licenselarge modeling suite
ASEFreeframework for setting up and analyzing atomistic simulations
Ab wtpFreeAlignment tool for SOLiD transcript reads
AbaqusRequires licensefinite-element package
AmberRequires licensemolecular dynamics
BEDToolsFreeBEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format
BLASTFreepackage for aligning nucleotide or amino acid sequences
BLATFreean alignment tool like BLAST, but it is structured differently.
BWAFreeA fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target).
BclConverterFreeConverts bcl files to Qseq files.
BioPerlFreeA community effort to produce Perl code which is useful in biology.
BioPythonFreeA set of freely available tools for biological computation written in Python by an international team of developers.
BioscopeSite licensethe pipeline stack that comes with the solid sequence platform
BowtieFreeBowtie is an ultrafast, memory-efficient short read aligner.
CASAVAIllumina's Consensus Assessment of Sequence and Variation (CASAVA) software
CASTEPRequires licenseelectronic structure calculation
CDOFreedata analysis
CESM1Freeglobal climate model
CP2KFreeatomistic and molecular simulations code
CPMDFreeplane-wave DFT
CS-RosettaFreede novo protein structure generation
CSAFreePython implementation of the Connection-set Algebra (Djurfeldt 2012)
Ccp4Freedetermining macromolecular structures by X-ray crystallography
CharmmRequires licenseatomistic and molecular simulations code
ClustalWFreepopular multiple sequence aligner
ComsolSite licenseCommercial Mulitphysics Similation software
ConcaterpillarFreeA hierarchical likelihood ratio test for phylogenetic congruence.
CootFreesoftware for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data
CufflinksFreeAssembles transcripts in RNA-Seq samples and calculates their abundances
CyanaSite licensebiological macromolecule structure calculation based on NMR conformational constraints
DDTSite licenseDebugger
DIANARequires licensecommercial FEM package
DacapoFreeplane-wave DFT
Daltonpowerful molecular electronic structure program.
DesmondFreemolecular dynamics package
EC-EarthFreeglobal climate model
EMBOSSFreeA free Open Source software analysis package developed for the molecular biology.
EMMAXA statistical test for large scale human or model organism association mapping accounting for the sample structure.
EMTOFreeExact Muffin-Tin Orbitals method, an electronic structure code based on the Green's function technique
EMTOxFreeExact Muffin-Tin Orbitals method (x), an electronic structure code based on the Green's function technique
ESPResSoFreemolecular dynamics of soft matter systems
Edgeunstructured CFD solver
EfieldRequires licensesimulation environment for electromagnetic simulations
ElkFreeall-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features
Environment modulesFreepackage to manage the systems and application software
... further results

See also

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