Software

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This page lists software in use at various SNIC centres.

 Research areaDescription
ABINITdensity-functional theory code
ABySSA parallel assembler for short read sequence data
ACMLefficient mathematics library
ANFOA parallel assembler for short read sequence data
ANNOVARFunctional annotation of genetic variants from high-throughput sequencing data
ANSYSlarge modeling suite
ARC clienttool for accessing the Grid resources
ASEframework for setting up and analyzing atomistic simulations
Ab wtpAlignment tool for SOLiD transcript reads
Abaqusfinite-element package
Ambermolecular dynamics
BEDToolsBEDTools is a software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format
BLASTpackage for aligning nucleotide or amino acid sequences
BLATan alignment tool like BLAST, but it is structured differently.
BWAA fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target).
BclConverterConverts bcl files to Qseq files.
BioPerlA community effort to produce Perl code which is useful in biology.
BioPythonA set of freely available tools for biological computation written in Python by an international team of developers.
Bioscopethe pipeline stack that comes with the solid sequence platform
BowtieBowtie is an ultrafast, memory-efficient short read aligner.
CASAVAIllumina's Consensus Assessment of Sequence and Variation (CASAVA) software
CASTEPelectronic structure calculation
CDOdata analysis
CESM1global climate model
CP2Katomistic and molecular simulations code
CPMDplane-wave DFT
CS-Rosettade novo protein structure generation
CSAPython implementation of the Connection-set Algebra (Djurfeldt 2012)
Ccp4determining macromolecular structures by X-ray crystallography
Charmmatomistic and molecular simulations code
ClustalWpopular multiple sequence aligner
ComsolCommercial Mulitphysics Similation software
ConcaterpillarA hierarchical likelihood ratio test for phylogenetic congruence.
Cootsoftware for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data
CufflinksAssembles transcripts in RNA-Seq samples and calculates their abundances
Cyanabiological macromolecule structure calculation based on NMR conformational constraints
DDTDebugger
DIANAcommercial FEM package
Dacapoplane-wave DFT
Daltonpowerful molecular electronic structure program.
Desmondmolecular dynamics package
EC-Earthglobal climate model
EMBOSSA 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.
EMTOExact Muffin-Tin Orbitals method, an electronic structure code based on the Green's function technique
EMTOxExact Muffin-Tin Orbitals method (x), an electronic structure code based on the Green's function technique
ESPResSomolecular dynamics of soft matter systems
Edgeunstructured CFD solver
Efieldsimulation environment for electromagnetic simulations
Elkall-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features
... further results

See also