Software

This page lists software in use at various SNIC centres.

	Field	Description
ABINIT	Computational chemistry Computational materials science	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
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 chemistry Computational materials science	electronic structure calculation
CDO	Climate research	data analysis
CESM1	Climate research	global climate model
CP2K	Computational chemistry Computational materials science	atomistic and molecular simulations code
CPMD	Computational chemistry Computational materials science	plane-wave DFT
CS-Rosetta	Bioinformatics	de novo protein structure generation
CSA	Bioinformatics	Python implementation of the Connection-set Algebra (Djurfeldt 2012)
Ccp4	Visualisation Structural biology	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	Visualisation Structural biology	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 chemistry Computational materials science	plane-wave DFT
Dalton	Computational chemistry	powerful molecular electronic structure program.
Desmond	Computational chemistry Molecular dynamics	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 chemistry Computational materials science	molecular dynamics of soft matter systems
Edge	Computational fluid dynamics	unstructured CFD solver
Efield	Computational electromagnetics	simulation environment for electromagnetic simulations
Elk	Computational chemistry Computational materials science	all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features
Environment modules	System tool	package to manage the systems and application software
... further results

See also

• Category:Software.