Software

This page lists software in use at various SNIC centres.

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

See also

• Category:Software.