Software

This page lists software in use at various SNIC centres.

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

See also

• Category:Software.