Fields of science

• Biosciences
• Chemistry
• Computational drug design
• Computational fluid dynamics
• Earth sciences
• Language research
• Mathematics
• Nanoscience
• Physics
• Statistics
• Structural analysis
• Visualisation

Biosciences		Back to top
ABySS	De-novo sequece assembly program	A
BEAST	A program for Bayesian MCMC analysis of molecular sequences.	P
BEDTools	Bedtools: a flexible suite of utilities for comparing genomic features.	P
BLAST	Sequence database homology search	A
BLAT	Blat is an alignment tool like BLAST	P
Bowtie	Aligns short DNA reads to genomic sequence	P
Bowtie2	NGS short read mapper.	A
BWA	Sequence assembly	P
CD-HIT	Sequence clustering tool	A
CHARMM	Molecular meachanics and dynamics	A
Chipster	Analysis software for DNA microarray data	P
ClustalW	Multiple sequence alignment	G
Cufflinks	RNA-Seq ananlysis tool	A
DHSMAP	LD-based fine mapping of genes	P
DiscoveryStudio	Molecular modeling program for proteins	A
EMBL	nucleotide sequences	P
EMBOSS	sequence analysis package	A
ExaML	Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI. (Implement RAxML)	P
exonerate	Sequence alignment program	A
FastQC	A quality control tool for high throughput sequence data.	P
genehunter	Parametric and nonparametric linkage analysis	G
GenomatixSuiteP	Promoter analysis software and database	A
gsnap	Short read mapping tool for NGS data.	A
haploassoc	Gene mapping	A
haploview	Gene mapping	A
HMMER	Profile HMMs for protein sequence analysis	A
Jalview	Sequence alignment editor	A
linkage	LINKAGE	G
Maestro	Versatile molecular modelling environenment especially for drug design	A
MAFFT	Multiple sequence aligment program.	A
Maq	Sequence assembly	P
Meme	Sequece motif detection tool.	A
Merlin	Genetic linkage analysis	G
MrBayes	Phylogenetics	A
Muscle	A fast and accurate sequence alignment program	P
NAMD	Molecular dynamics program	A
Nr_aa	The NR protein sequence database from NCBI	P
Nt_na	The NT nucleotide sequence database from NCBI	P
PairsDB	Protein sequence comparison database	P
PDB	3D structures	P
pedcheck	Check pedigree files for errors	G
Pfam	HMMs for protein families and domains	A
PHYLIP	Program package for phylogenteic analysis	G
phyml	PhyML is a phylogeny software based on the maximum-likelihood principle	P
Pise	Pise, a tool to generate Web interfaces	A
POY	Phylogenetics analysis	P
Prinseq	A quality control tool for high throughput sequence data.	P
PRINTS	motif fingerprints for protein families and domains	P
Prosite	patterns and profiles for protein families and domains	P
pseudomarker	Pseudomarker analysis of gene mapping data	A
RAxML	A program for inference of phylogenies using maximum likelihood methods	A
RefSeq	nucleotide sequences (mRNA and human genomic contigs)	P
Rosetta	Software suite for predicting, designing and docking protein structures.	A
SAMtools	SAM-muotoisten sekvenssirinnastusten käsittelyohjelma.	A
Seaview	Sequence editor	A
SHRiMP	NGS reference mapping tool	A
SimWalk2	Fast linkage analysis and haplotype determination	G
snphap	Gene Mapping	A
SOAPdenovo	De-novo sequece assembly program	A
SP-TREMBL	translations of EMBLs coding sequences, to be included in SwissProt	P
SSAHA	Hashing algorithm based tool for very fast matching and alignment of sequences.	A
stampy	Stampyis a package for the mapping of short reads from illumina sequencing machines onto a reference	P
SWISS-PROT	protein sequences	A
Sybyl	software package for molecular design and analysis	A
TMHMM	Prediction of transmembrane helices in proteins.	A
TNT	Fast parsimony program for phylogenetics	A
TopHat	splice junction mapper for RNA-Seq reads	P
TrEMBL	translations of EMBL	P
vcftools	Software for manipulating VCF files.	A
Velvet	Sequence assembler for short reads	A
Wise2	Ohjelma jolla verrattaan proteiinisekvenssiä tai HMM-proiilia DNA-sekvenssiin	A
Chemistry		Back to top
ADF	Quantum Chemistry (DFT)	A
Amber	Molecular dynamics	A
AutoDock	Docking of flexible molecules	A
Babel	Molecule file format conversion utility	A
CASTEP	Quantum mechanics (materials sciences)	A
CHARMM	Molecular meachanics and dynamics	A
ConQuest	Molecular structures search program (CSD)	A
corina	Generates 3D molecular structures from 2D database	A
CP2K	Versatile ab initio and classical molecular dynamics	A
CSD	Cambridge Structural Database (CSD)	A
Dmol3	Quantum chemistry ( DFT)	A
FFE	Tinker GUI	A
Gaussian	Quantum chemistry ( ab initio HF, DFT )	G
GOLD	Flexible protein-ligand docking	A
gOpenMol	Visualization and analysis of molecules	A
GPAW	Density functional theory	P
Gromacs	Versatile package to perform molecular dynamics	P
IsoStar	A Knowledge Base of Intermolecular Interactions (CSD)	A
Maestro	Versatile molecular modelling environenment especially for drug design	A
MaterialsStudio	Materials science program package	A
Mercury	Crystal structure viewing and analysing software. A part of the CSD-package.	A
Mogul	Statistics of molecular geometry (CSD)	A
Molden	MOLDEN a pre- and post processing program of molecular and electronic structure	A
Molpro	Quantum chemistry, especially ab initio	G
NAMD	Molecular dynamics program	A
NWChem	Computational chemistry (ab initio, DFT, MM/MD)	A
PERCH	PERCH NMR spectroscopy tool	A
PreQuest	Create CSD-format molecule databases (CSD)	A
Reaxys	Database for chemistry	A
Rosetta	Software suite for predicting, designing and docking protein structures.	A
Rotate	Conformer generator for acylic molecules and fragments	A
siesta	Electronic structure, DFT, local basis set	A
SOMA2	SOMA2-WWW-interface	P
SuperStar	Protein-ligand interactions prediction (CSD)	A
Sybyl	software package for molecular design and analysis	A
TmoleX	GUI for Turbomole	A
TURBOMOLE	quantum chemistry (ab initio, DFT)	A
VASP	Plane Wave DFT, dynamics	A
VISTA	Display tool for geometric data (CSD)	A
VMD	Biomolecular visualization and modeling	A
Computational drug design		Back to top
AutoDock	Docking of flexible molecules	A
corina	Generates 3D molecular structures from 2D database	A
GOLD	Flexible protein-ligand docking	A
Rotate	Conformer generator for acylic molecules and fragments	A
SOMA2	SOMA2-WWW-interface	P
Computational fluid dynamics		Back to top
Ansys_CFX	Computational Fluid Dynamics software	A
ComsolMultiphys	Multiphysical modelling	A
Elmer	Multiphysical simulation software (FEM)	P
Fluent	Computational Fluid Dynamics software	A
Gambit	Computational Fluid Dynamics preprocessor	A
ICEMCFD	CFD Preprocessor	A
netcdf	Common data format for array oriented scientific data.	P
OpenFOAM	OpenSource CFD Package	P
Earth sciences		Back to top
afterburner	Postprocessing tool for e.g. ECHAM5-data	P
ArcGis	Geographic Information System Program	A
CDO	Program for analysis of clilmate/meterological data	P
Elmer	Multiphysical simulation software (FEM)	P
GrADS	Grid analysis and display system	A
MapInfo	Geographic information System	A
MPI-OM	Ocean model.	A
ncdump	Convert netCDF files to ASCII form	P
NCEP	meteorological reanalysis data	A
ncgen	From a CDL file generate a netCDF file, a C program, or a Fortran program	P
NCL graphics	Visualization language for atmospheric data	P
ncview	program for visualising NetCDF-files	P
netcdf	Common data format for array oriented scientific data.	P
Language research		Back to top
acquis	The JRC-Acquis Multilingual Parallel Corpus	P
amph	Ajatella, miettiä, pohtia, harkita Corpus	A
childes	Child language exchange database	P
dancg	Lingsoft Danish parser	A
dma	Digital Morphology Archives	A
en-fdg	Connexor Machinese Syntax for English	A
engcg	Lingsoft English parser	A
fbc	Finnish Broadcast Corpus	A
ffmpeg	FFmpeg is used to to record, convert and stream audio and video.	P
fi-fdg	Connexor Machinese Syntax for Finnish	A
fintwol	Lingsoft Finnish parser	A
fstc	Finnish-Swedish Textcollection	A
ftc	Finnish Text Collection	A
gertwol	Lingsoft German parser	A
hcs	The Helsinki Corpus of Swahili	A
hfst	Helsinki Finite-State Transducer Technology	P
hfst-language-tools	Helsinki Finite-State Transducer Language Tools	P
kra	Jyväskylä Corpus of Middle-French	A
ksfpc	KOTUS Swedish-Finnish Parallel Corpus	P
lat	Audiovisual corpus environment	A
lemmieshell	A command line tool for querying the Language Bank corpora	A
libxml2	libxml2 (2.7.8) and libxslt (1.1.26) libraries and standalone command line tools	P
mrc-uhlcs	A collection of small corpora of multiple languages	A
nnotwol	Lingsoft Nynorsk parser	A
nobcg	Lingsoft Bokmål parser	A
nooj	NooJ is a linguistic development environment that includes large-coverage dictionaries and grammars.	P
ota	A collection of Oxford Text Archive texts	P
oulu	Oulu corpus	A
parole-de	PAROLE corpus of the German language	A
parole-fi	PAROLE corpus of the Finnish language	A
parole-sv	PAROLE corpus of the Swedish language	A
pc-parse	A set of tools for morphological and syntactic analysis	A
rustwol	Lingsoft Russian parser	A
saxon	Saxon XSLT processor	A
sfnet	SFNET discussion group corpus	A
sicstus prolog	SICStus Prolog is a state-of-the-art, ISO standard compliant, Prolog development system	A
susanne	The SUSANNE corpus of English	P
sv-fdg	Connexor Machinese Syntax for Swedish	A
swecg	Lingsoft Swedish parser	A
textmorfo	Kielikone Shallow parser for Finnish syntax	A
wordnet	Lexical database of English	P
www-lemmie	A web interface for querying the Language Bank corpora	A
Mathematics		Back to top
ComsolMultiphys	Multiphysical modelling	A
IDL	interactive analysis and visualization of data	R
IMSL	Fortran Numerical Library	A
Magma	Dense linear algebra library with GPU acceleration	P
Maple	symbolic mathematics	A
Mathematica	Symbolic mathematics	P
Matlab	Matrix-based program for numeric computation	A
NumPy	Library for scientific computing with Python	P
P_ARPACK	Large Eigenvalue problems	A
PESSL	parallel engineering and scientific subroutine lib	A
Nanoscience		Back to top
GPAW	Density functional theory	P
siesta	Electronic structure, DFT, local basis set	A
TURBOMOLE	quantum chemistry (ab initio, DFT)	A
VASP	Plane Wave DFT, dynamics	A
Physics		Back to top
CASTEP	Quantum mechanics (materials sciences)	A
echam5	Atmosphere model.	A
Elmer	Multiphysical simulation software (FEM)	P
GPAW	Density functional theory	P
MaterialsStudio	Materials science program package	A
MPI-OM	Ocean model.	A
netcdf	Common data format for array oriented scientific data.	P
OASIS3	Climate model coupling libraries and tools	P
siesta	Electronic structure, DFT, local basis set	A
VASP	Plane Wave DFT, dynamics	A
Statistics		Back to top
JAGS	Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulations.	A
MySQL-client	MySQL client software	A
R	Statistical Computing	P
Structural analysis		Back to top
Abaqus Expanded Teaching Edition	Structural analysis, finite element method	A
Abaqus Research Edition	Structural analysis, finite element method	A
ANSYS Academic Research	Structural analysis, finite element method	A
LMS Imagine.Lab AMESim	The integrated platform for 1D multi-domain system simulation	A
LMS Virtual.Lab	LMS Virtual.Lab offers an integrated software suite to simulate the performance of mechanical system	A
MSC.Software University FEA Bundle	Structural analysis, finite element method	A
MSC.Software University Motion Bundle	Structural analysis, multi-body dynamics	A
Visualisation		Back to top
FreeNX	Remote Desktop for fast remote graphics from CSC s servers	A
gOpenMol	Visualization and analysis of molecules	A
IDL	interactive analysis and visualization of data	R
NCL graphics	Visualization language for atmospheric data	P
netcdf	Common data format for array oriented scientific data.	P
Paraview	A Parallel Visualization Application	P
VisiQuest	Image prosessing program	A