Applications by availability
Applications available on
Interactive web applications available on
Roihu
- Abaqus — Dassault Systemes' SIMULIA academic research suite
- ABySS — De novo, parallel, paired-end sequence assembler
- AdmixTools — Inference of population admixture from f-statistics
- ADMIXTURE — Maximum-likelihood estimation of individual ancestries from SNP data
- Amber — Molecular dynamics suite
- AMS — Modelling suite providing the ADF engine
- AMS-GUI — AMS integrated GUI
- ANGSD — Analysis of next-generation sequencing data via genotype likelihoods
- Ansys — Ansys Academic research CFD
- antiSMASH — Detection of secondary-metabolite biosynthesis gene clusters in microbial genomes
- ASTRAL — Coalescent-based species-tree estimation from gene trees
- AUGUSTUS — Gene prediction in eukaryotic genomic sequences
- Bakta — Rapid and standardized annotation of bacterial genomes, MAGs and plasmids
- BamTools — Tools for working with BAM formatted files
- Barrnap — Rapid ribosomal RNA (rRNA) prediction
- BayeScan — Tool for identifying candidate loci under natural selection based on allele frequencies in populations
- BBMap — BBTools short-read aligner and sequence-processing suite
- BCFtools — Variant calling and VCF/BCF manipulation
- BEDOPS — Set operations on genomic intervals (BED)
- BEDTools — Genome arithmetic on BED/VCF/GFF intervals
- Bio-apps — Access module to a collection of applications and software often used in biosciences
- 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
- Blender — 3D modeling, visualization and rendering software
- Bowtie — Ultrafast, memory-efficient short read aligner
- Bowtie2 — Short read aligner
- Bracken — Species abundance estimation from Kraken2 output
- BRAKER — Automatic genome annotation pipeline for eukaryotes
- BUSCO — Genome/transcriptome completeness assessment via orthologs
- BWA — Short read aligner
- bwa-mem2 — Faster successor to bwa mem
- Canu — Long-read (PacBio/Nanopore) genome assembler
- CD-HIT — Sequence clustering and redundancy removal tool
- CDO — Command line tools to manipulate and analyse Climate and NWP model Data
- CheckM2 — Genome quality assessment via machine learning
- Chipster_genomes — Tool to download aligner indexes used by Chipster to Roihu
- CloudCompare — for visualizing, editing and processing point clouds
- CLUMPP — Alignment of replicate cluster assignments from population-structure analyses
- Clustal Omega — Multiple sequence alignment
- ClustalW — Multiple sequence alignment
- compute-sanitizer — Functional correctness checking suite included in the CUDA toolkit
- COMSOL Multiphysics — General-purpose simulation software
- COSMO-RS — Toolbox for the prediction of fluid phase thermodynamic properties using the COSMO-RS model
- CP2K — DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
- cProfile — Built-in profiler for Python programs
- CSD — Cambridge Structural Database and software for searching and analysing crystal structures
- cuda-gdb — Nvidia extension of the GNU debugger GDB
- Cufflinks — Transcript assembly and differential expression for RNA-Seq
- Cutadapt — Trimming high-throughput sequencing reads
- deepTools — Tools for exploring deep-sequencing coverage data
- demix_check — Check mSWEEP/mGEMS cluster assignments of demixed reads
- Diamond — Sequence similarity search tool for proteins and nucleotides
- Dorado — GPU-accelerated Oxford Nanopore basecaller
- eBay's tsv-utils — Utilities for manipulating large tabular data files
- eggNOG-mapper — Functional annotation of sequences via orthology (eggNOG)
- Elmer — Open source multi-physics FEM package
- EMBOSS — Toolkit for classical sequence analysis
- Entrez Direct — Entrez direct - command line tool to search and retrieve data from NCBI
- Exonerate — A generic tool for pairwise sequence comparison
- fastp — Fast all-in-one FASTQ preprocessing and QC
- FastQC — Quality control tool for high throughput sequence data
- FASTX-Toolkit — FASTA/FASTQ short-read preprocessing tools
- FDSTools — Noise analysis and allele calling for forensic DNA sequencing data
- FFmpeg — Tools and libraries for recording, converting and streaming audio and video
- Foldseek — Fast protein structure search and clustering
- Freebayes — Genetic variant detector
- gapseq — Genome-scale metabolic network reconstruction and analysis
- GATK — Genome Analysis Toolkit for variant discovery
- Gaussian — Versatile computational chemistry package
- GDAL — for geospatial data formats
- gdb — GNU debugger for compiled programs
- GetOrganelle — Assembly of organelle genomes from whole-genome sequencing data
- GOLD — Protein-ligand docking program
- 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
- GTDB-Tk — Taxonomic classification of bacterial and archaeal genomes using the GTDB
- HeLI-OTS — Off-the-shelf language identifier with language models for 220 languages
- hifiasm — Haplotype-resolved de novo assembler for PacBio HiFi and ONT reads
- HISAT2 — Spliced aligner for RNA-seq and DNA reads
- HMMER — Toolkit to create and use sequence profile hidden Markov models
- HUMAnN — Profiling microbial pathways with metagenomic data
- HybPiper — Target-capture (Hyb-Seq) locus recovery for phylogenomics
- HyperQueue — Scheduler for sub-node tasks
- HyPhy — Hypothesis testing on phylogenies (selection analysis)
- IDL — Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
- IGV — Integrative Genomics Viewer - interactive genome browser
- Illumina BaseSpace — Command line client for retrieving data from the Illumina BaseSpace environment
- inStrain — Strain-level population genomics from metagenomic mappings
- 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)
- IQ-TREE — Maximum-likelihood phylogenetic inference
- JAX — Autograd and XLA, brought together for high-performance machine learning
- Jellyfish — Fast k-mer counting
- Julia Language — High-level, high-performance dynamic programming language for numerical computing
- kp-spell (enchant) — Finnish and Swedish spell-checking via the enchant interface
- Kraken — Taxonomic sequence classification system
- 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
- MACS2/3 — ChIP-Seq analysis tool
- Maestro — Versatile drug discovery and materials modeling suite
- MAFFT — Multiple sequence alignment
- Mash — Fast genome/metagenome distance estimation (MinHash)
- MATLAB — High-level technical computing language
- medaka — Nanopore consensus and variant calling
- MedeA — Materials modeling and simulation environment
- Megahit — Metagenomics assembly
- MEME Suite — Motif discovery and analysis (MEME Suite)
- MetaBAT — Metagenome binning (MetaBAT2)
- MetaHipMer2 — GPU-accelerated metagenome assembly
- MetaPhlAn — Profiling the composition of microbial communities with metagenomic data
- MICOM — Metabolic modelling of microbial communities
- minibwa — Short-read aligner, successor to BWA-MEM
- Minimap2 — Short read aligner
- MMseqs2 — Very fast protein search and clustering
- 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
- MUMmer — Genome alignment (MUMmer)
- MUSCLE — Multiple sequence alignment (v3)
- MUSCLE5 — Multiple sequence alignment (v5)
- NAMD — Highly scalable classical molecular dynamics
- NCBI C++ Toolkit — NCBI C++ Toolkit libraries and command-line applications
- ncu — Nvidia CUDA kernel profiler
- Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
- nsys — Nvidia GPU and CPU profiler
- Octave — High-level interpreted language for numerical computations
- Open Babel — Program to interconvert file formats currently used in molecular modeling
- OpenDroneMap (ODM) — for processing aerial drone imagery
- OpenFOAM — OpenFOAM® is the leading free, open source software for computational fluid dynamics (CFD)
- openSMILE — Toolkit for extracting audio features for speech and music analysis
- ORCA — General-purpose quantum chemistry package
- Orfeo ToolBox — for remote sensing applications
- PANNZER2/SANSPANZ — Automatic protein annotation tool
- ParaView — Free open-source visualization application
- PDAL — for point cloud translations and processing
- pdb — Built-in Python debugger
- perf — Command line tool for performance analysis
- PHYLIP — PHYLIP phylogeny inference package
- Picard Tools — Tools for working with SAM,BAM,CRAM and VCF files
- PLUMED — Library and tools for enhanced sampling methods
- Praat — Toolkit for annotating, processing and analysing speech and other audio samples
- Prodigal — Prokaryotic gene prediction
- Prokka — Rapid prokaryotic genome annotation
- Python — The programming language and its modules at CSC
- Python Data — Collection of Python libraries for data analytics and machine learning
- Python-geo — Python libraries for spatial analysis
- PyTorch — Machine learning framework for Python
- QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- QIIME — Package for microbial community analysis of amplicon sequencing data
- Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale
- R for GIS — R spatial analysis libraries
- r-env — R and RStudio Server
- RAxML — Program for inferring phylogenies with likelihood
- RAxML-NG — Maximum-likelihood phylogenetic inference (RAxML-NG)
- RevBayes — Bayesian phylogenetic inference with probabilistic graphical models
- Roary — Pan genome pipeline
- RStudio IDE — Integrated development environment for R
- run_dbcan — Automated carbohydrate-active enzyme (CAZyme) annotation
- SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- SALMON — Program to produce transcript-level quantification estimates from RNA-seq data
- SameStr — Strain-level sharing analysis from metagenomic SNV profiles
- SAMtools — Utilities for managing SAM/BAM formatted alignment files
- SeqKit — Cross-platform FASTA/FASTQ toolkit
- Seqtk — Tool for processing sequences in the FASTA or FASTQ format
- Snakemake — Snakemake is a scientific workflow management system for creating scalable, portable, and reproducible workflows
- SNAP — for remote sensing applications
- SortMeRNA — Filtering and sorting of rRNA reads from (meta)transcriptomic data
- SPAdes — Genome assembly
- SRA Toolkit — NCBI SRA Toolkit for accessing and converting SRA data
- STAR — Short read aligner
- Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software
- SteadierCom — Steady-state metabolic simulation of microbial communities
- StrAuto — Automation and parallelization of STRUCTURE analysis
- StringTie — Transcript assembly and quantification for RNA-Seq
- Structure — Inference of population structure in genetics
- Structure Harvester — Post-processing of STRUCTURE results (Evanno method)
- TensorFlow — Deep learning library for Python
- TopHat — Splice junction mapper for RNA-Seq reads
- trankit — Transformer-based Python toolkit for multilingual Natural Language Processing (NLP)
- Trimmomatic — Trim Illumina paired-end and single-read data
- Trinity — Transcriptome assembly tool
- TURBOMOLE — Fast and robust quantum chemistry program package
- UDPipe — Trainable pipeline for tokenization, tagging, lemmatization and dependency parsing
- VASP — Ab initio DFT electronic structures
- VCFtools — VCF manipulation and statistics
- VisIt — Free open-source visualization application
- vLLM — A fast and easy-to-use library for LLM inference and serving
- VMD — Molecular visualization program
- vrt-tools — Tools for converting VRT (Vertical Text) corpus files
- VSEARCH — Versatile sequence search and clustering
- WhiteboxTools — an advanced geospatial data analysis platform
- wtdbg2 — Fast assembler for long-read data
- XHMM (eXome-Hidden Markov Model) — Copy number variation calling from targeted sequencing data
- yak — K-mer counting and k-mer based quality evaluation of reads and assemblies
- Zonation — Spatial conservation prioritization framework
LUMI
- Accelerated visualization — A selection of GPU accelerated visualization applications
- Amber — Molecular dynamics suite
- Blender — 3D modeling, visualization and rendering software
- Cirq-on-iqm — open-source cirq adapter for quantum computing
- CP2K — DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
- Desktop — Remote desktop environment
- Elmer — Open source multi-physics FEM package
- GDAL — for geospatial data formats
- Geoconda — Python libraries for spatial analysis
- GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- GROMACS — Fast and versatile classical molecular dynamics
- HADDOCK3 — High Ambiguity Driven biomolecular DOCKing
- HyperQueue — Scheduler for sub-node tasks
- JAX — Autograd and XLA, brought together for high-performance machine learning
- Julia Language — High-level, high-performance dynamic programming language for numerical computing
- Julia-Jupyter — Interactive computational environment for Julia
- Jupyter — Interactive computational environment for Python
- LAMMPS — Fast molecular dynamics engine with large force field selection
- Maestro — Versatile drug discovery and materials modeling suite
- MATLAB — High-level technical computing language
- NAMD — Highly scalable classical molecular dynamics
- Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
- NMRLipids — NMRLipids databank containing MD simulations
- OpenFOAM — OpenFOAM® is the leading free, open source software for computational fluid dynamics (CFD)
- PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows
- ParaView — Free open-source visualization application
- PDAL — for point cloud translations and processing
- Pennylane — Free open-source software framework for quantum machine learning and quantum computing
- perf — Command line tool for performance analysis
- PLUMED — Library and tools for enhanced sampling methods
- QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- Qiskit — open-source toolkit for useful quantum computing
- Qiskit-on-iqm — open-source qiskit adapter for quantum computing
- Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale
- SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software
- TensorBoard — The visualization toolkit for TensorFlow
- TensorFlow — Deep learning library for Python
- VisIt — Free open-source visualization application
- Visual Studio Code — Source code editor
- WhiteboxTools — an advanced geospatial data analysis platform
Roihu web interface
- Accelerated visualization — A selection of GPU accelerated visualization applications
- Blender — 3D modeling, visualization and rendering software
- CloudCompare — for visualizing, editing and processing point clouds
- COMSOL Multiphysics — General-purpose simulation software
- Desktop — Remote desktop environment
- Grace — Plotting tool for xvg-files in particular
- GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- Julia-Jupyter — Interactive computational environment for Julia
- Jupyter — Interactive computational environment for Python
- Jupyter for courses — A version of the Jupyter app for course environments
- MATLAB — High-level technical computing language
- Molden — Processing program for molecular and electronic structure calculations
- ParaView — Free open-source visualization application
- QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- RStudio IDE — Integrated development environment for R
- SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- SNAP — for remote sensing applications
- TensorBoard — The visualization toolkit for TensorFlow
- VisIt — Free open-source visualization application
- Visual Studio Code — Source code editor
- VMD — Molecular visualization program
- Zonation — Spatial conservation prioritization framework
LUMI web interface
- Accelerated visualization — A selection of GPU accelerated visualization applications
- Blender — 3D modeling, visualization and rendering software
- Desktop — Remote desktop environment
- GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- Julia-Jupyter — Interactive computational environment for Julia
- Jupyter — Interactive computational environment for Python
- MATLAB — High-level technical computing language
- ParaView — Free open-source visualization application
- QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
- TensorBoard — The visualization toolkit for TensorFlow
- VisIt — Free open-source visualization application
- Visual Studio Code — Source code editor