Applications

Applications in alphabetical order

Abaqus Dassault Systemes' SIMULIA academic research suite
Accelerated visualization A selection of GPU accelerated visualization applications
Amber Molecular dynamics suite
Ames Stereo Pipeline for processing stereo images
AMS-GUI AMS integrated GUI
AMS Modelling suite providing engines like ADF, BAND, DFTB and MOPAC
ANSYS ANSYS Academic engineering simulation software suite
ArcGIS General purpose GIS software family for viewing, editing and analysing geospatial data
BAMtools Tools for working with BAM formatted files
BayeScan Tool for identifying candidate loci under natural selection based on allele frequencies in populations
Bioconda Package manger for installing bioinformatics software
BioPerl Perl environment with bioperl extension
BioPython Python environment with biopython and other bioinformatics related Python libraries
BLAST Sequence similarity search tool for nucleotides and proteins
Bowtie2 Short read aligner
BRAKER Automatic genome annotator for eucaryots
BWA Short read aligner
CD-hit Sequence clustering and redundancy removal tool
Chipster Easy-to-use analysis platform for RNA-seq, single cell RNA-seq and other NGS data
Chipster_genomes Tool to download aligner indexes used by Chipster to Puhti
CloudCompare for visualizing, editing and processing poing clouds
COMSOL Multiphysics General-purpose simulation software
CP2k DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
CSD Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools
Cutadapt Trimming high-throughput sequencing reads
DDT Parallel debugger
Desktop Remote desktop environment
Diamond Sequence similarity search tool for proteins and nucloeotides
Discovery Studio Protein modeling environment
eBay's tsv-tools Utilities for manipulating large tabular data files
Edirect Entrez direct - command line tool to search and retrieve data from NCBI
Elmer Open source multi-physics FEM package
EMBOSS Toolkit for classical sequence analysis
Exonerate A generic tool for pairwise sequence comparison
FastQC Quality control tool for high throughput sequence data
Finnish Tagtools Finnish Tagtools
finnish-parse Dependency Parser for Finnish
FORCE for mass-processing of medium-resolution satellite images
Freebayes Genetic variant detector
Gaussian Versatile computational chemistry package
GDAL for geospatial data formats
Geoconda - Python spatial analysis libraries
GOLD Protein Ligand Docking Software
GPAW Versatile DFT package
Grace Plotting tool for xvg-files in particular
GRASS GIS General purpose GIS software family for viewing, editing and analysing geospatial data
Gromacs Fast and versatile classical molecular dynamics
HFST-fi Helsinki Finite-State Technology for Finnish
HFST-sv Helsinki Finite-State Technology for Swedish
HFST Helsinki Finite-State Transducer Technology
HMMER Toolkit to create and use sequence profile hidden Markov models
HUMAnN Profiling microbial pathways with metagenomic data
HyperQueue Scheduler for sub-node tasks
IDL Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
Illumina BaseSpace Command line client for retrieving data from the Illumina BaseSpace environment
InterProScan Protein signature/motif search tool
Ipyrad toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS)
JAX Autograd and XLA, brought together for high-performance machine learning
Julia-Jupyter Interactive computational environment with Julia
Julia High-level, high-performance dynamic programming language for numerical computing
Jupyter for courses A version of the Jupyter app for course environments
Jupyter Interactive computational environment with Python
Kaldi Kaldi Speech Recognition Toolkit
Kraken2 Taxonomic sequence classification system
Krona Visualization tool for taxonomic classification and other hierarchical data
LAMMPS Fast molecular dynamics engine with large force field selection
LAStools for LiDAR datasets
Lazypipe A stand-alone pipeline for identifying viruses in host-associated or environmental samples
MACS2 ChIP-Seq analysis tool
Maestro Versatile drug discovery and materials modeling suite
Materials Studio Versatile materials modeling suite
MATLAB High-level technical computing language
MaxQuant A proteomics software for processing of Mass-spectromtery data
Megahit Metagenomics assembly
MetaPhlAn Profiling the composition of microbial communities with metagenomic data
Minimap2 Short read aligner
MIRA Whole genome shotgun and EST sequence Assembler
MOLDEN Processing program for molecular and electronic structure calculations
MOLPRO Package for accurate ab initio quantum chemistry calculations
Mothur Package for microbial community analysis of amplicon sequencing data
MrBayes Program for inferring phylogenies using Bayesian methods
MySQL MySQL database client.
NAMD Highly scalable classical molecular dynamics
NWChem A computational chemistry software package designed to perform well on parallel HPC systems
Octave High-level interpreted language for numerical computations
Open Babel Program to interconvert file formats currently used in molecular modeling
OpenDroneMap for processing aerial drone imagery
OpenFOAM Open source C++ tool box for continuum mechanics problems
ORCA General purpose quantum chemistry package
Orfeo ToolBox for remote sensing applications
PALM Meteorological model system for atmospheric and oceanic boundary-layer flows
Pannzer Automatic protein annotation tool
ParaView Free open-source visualization application
PCL for 2D/3D image and point cloud processing
PDAL for point cloud translations and processing
Picard Tools for working with SAM,BAM,CRAM and VCF files
Plumed Library and tools for enhanced sampling methods
Prokka Rapid prokaryotic genome annotation
Python Data Collection of Python libraries for data analytics and machine learning
Python programming language and its modules at CSC
PyTorch Machine learning framework for Python
QGIS General purpose GIS software family for viewing, editing and analysing geospatial data
QIIME2 Package for microbial community analysis of amplicon sequencing data
R for GIS R spataial analysis libraries
r-env R, RStudio Server, SAGA and TensorFlow
RAPIDS Suite of libraries for data analytics and machine learning on GPUs
RAxML Program for inferring phylogenies with likelihood
Roary Pan genome pipeline
RStudio Integrated development environment for R
SAGA GIS General purpose GIS software family for viewing, editing and analysing geospatial data
SageMath Free open-source mathematics software system
Salmon Program to produce transcript-level quantification estimates from RNA-seq data
Samtools Utilities for managing SAM/BAM formatted alignment files
Sen2Cor for atmospheric-, terrain and cirrus correction of the Sentinel-2 products
Sen2mosaic for download, preprocessing and mosaicing of Sentinel-2 products
Seqtk Tool for processing sequences in the FASTA or FASTQ format
SNAP for remote sensing applications
SPAdes Genome assembly
Spark High-performance distributed computing framework
Stacks Pipeline for building loci from short-read sequences (e.g. RAD-seq data)
Star-CCM+ Computational Fluid Dynamics software by Siemens Digital Industries Software
STAR Short read aligner
Structure Inference of population structure in genetics
TensorBoard The visualization toolkit for TensorFlow
TensorFlow Deep learning library for Python
TmoleX GUI for setting up and analyzing TURBOMOLE jobs
Tophat Splice junction mapper for RNA-Seq reads
Trinity Traskriptome assembly tool
Turbomole Efficient program package for electronic structure calculations
UDPipe UDPipe Kielipankki version
VASP Ab initio DFT electronic structures
Velvet Genome assembler
VirusDetect Virus identification with sRNA data
VisIt Free open-source visualization application
Visual Studio Code Source code editor
VMD Molecular visualization program
WhiteboxTools an advanced geospatial data analysis platform
wtdbg2 Fast assembler for long-read data
XHMM Copy number variation calling from targeted sequencing data
Zonation Spatial conservation prioritization framework