Table of Contents

Applications in alphabetical order

  • Abaqus Dassault Systemes' SIMULIA academic research suite
  • Amber Molecular dynamics suite
  • AMS Modelling suite providing engines like ADF, BAND, DFTB and MOPAC
  • ANSYS ANSYS Academic engineering simulation software suite
  • ArcGIS ArcGIS software suite for working with spatial 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
  • BWA Short read aligner
  • CD-hit Sequence clustering and redundancy removal tool
  • CFDEMcoupling Open source toolbox for CFD-DEM coupling
  • ChEMBL Database of bioactive molecules.
  • 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
  • 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
  • DDT Parallel debugger
  • 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 All-in-one command line tool for mass-processing of medium-resolution satellite images
  • Freebayes Genetic variant detector
  • Gaussian Versatile computational chemistry package
  • GDAL Translator library for geospatial data formats
  • Geoconda Spatial analysis libraries for Python, QGIS, GDAL and LasTools
  • GOLD Protein Ligand Docking Software
  • GPAW Versatile DFT package
  • Grace Plotting tool for xvg-files in particular
  • 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
  • HUMAnN2 Profiling microbial pathways with metagenomic data
  • 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)
  • Julia High-level, high-performance dynamic programming language for numerical computing
  • 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 Toolbox for LiDAR datasets
  • Lazypipe A stand-alone pipeline for identifying viruses in host-associated or environmental samples
  • LS-DYNA General-purpose finite element program
  • MACS2 ChIP-Seq analysis tool
  • Maestro Versatile drug discovery and materials modeling suite
  • Mapnik Open source toolkit for rendering maps
  • Materials Studio Versatile materials modeling suite
  • MATLAB High-level technical computing language
  • MaxQuant A proteomics software for processing of Mass-spectromtery data
  • Megahit Metagenomics assebly
  • 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
  • MXNet Deep learning library for Python
  • MySQL MySQL database client.
  • NAMD Highly scalable classical molecular dynamics
  • Nektar++ Spectral/hp element framework
  • NoMachine Remote Desktop enabling fast graphics without X-emulators
  • 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 open source command line toolkit for processing aerial drone imagery
  • OpenFOAM Open source C++ tool box for continuum mechanics problems
  • ORCA General purpose quantum chemistry package
  • Orfeo ToolBox Open source toolbox for processing high resolution optical, multispectral and radar images
  • PALM Meteorological model system for atmospheric and oceanic boundary-layer flows
  • Pannzer Automatic protein annotation tool
  • ParaView Free open-source visualization application
  • PDAL open source command line application 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
  • PyTorch Machine learning framework for Python
  • QGIS GIS application for viewing, editing, and analysing geospatial data
  • QIIME2 Package for microbial community analysis of amplicon sequencing data
  • R for GIS Documentation on the GIS libraries for R
  • r-env-singularity R, RStudio Server and SAGA (Singularity container)
  • 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
  • R Open-source language and environment for statistical analysis and graphics
  • SAGA GIS GIS application for spatial data editing and analysis
  • 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 Stand-alone processor for the Sentinel-2 satellite
  • Seqtk Tool for processing sequences in the FASTA or FASTQ format
  • SNAP Remote sensing toolbox for satellites
  • Sofi3d Application for 3D Finite-Difference Seismic Wave Simulation
  • Solaris Open source deep learning pipeline for geospatial imagery
  • SPAdes Genome assembly
  • Spark High-performance distributed computing framework
  • SPLITS Software package to analyze time series of remotely sensed parameters
  • 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
  • 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
  • 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