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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

Applications

Cannot find the application you are looking for?

  • See here for ways to install software yourself .
  • You may also contact CSC Service Desk with your software installation request. Given enough requests, we may consider pre-installing a particular application, or purchasing a license for it if the software in question is proprietary.
  • Although we cannot promise to pre-install all requested applications, CSC Service Desk is happy to support you in installing software yourself.

Applications in alphabetical order

A

  • Abaqus — Dassault Systemes' SIMULIA academic research suite
  • ABySS — De novo, parallel, paired-end sequence assembler
  • Accelerated visualization — A selection of GPU accelerated visualization applications
  • AdmixTools — Inference of population admixture from f-statistics
  • ADMIXTURE — Maximum-likelihood estimation of individual ancestries from SNP data
  • Alphafold — Protein 3D structure prediction
  • 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
  • ArcGIS Python API — Spatial analysis and data science
  • ASTRAL — Coalescent-based species-tree estimation from gene trees
  • AUGUSTUS — Gene prediction in eukaryotic genomic sequences

B

  • 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

C

  • 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  — 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
  • Cirq-on-iqm — open-source cirq adapter for quantum computing
  • 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
  • CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
  • CSD — Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools
  • cuda-gdb — Nvidia extension of the GNU debugger GDB
  • Cufflinks — Transcript assembly and differential expression for RNA-Seq
  • Cutadapt — Trimming high-throughput sequencing reads

D

  • DDT — Parallel debugger
  • deepTools — Tools for exploring deep-sequencing coverage data
  • Desktop — Remote desktop environment
  • Diamond — Sequence similarity search tool for proteins and nucleotides
  • Dorado — GPU-accelerated Oxford Nanopore basecaller

E

  • 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

F

  • 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
  • FFmpeg — Tools and libraries for recording, converting and streaming audio and video
  • Finnish Tagtools  — Finnish Tagtools
  • FireWorks — FireWorks is a free, open-source tool for defining, managing and executing workflows with multiple steps and complex dependencies
  • Freebayes — Genetic variant detector

G

  • 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
  • Geoconda — Python libraries for spatial analysis
  • GetOrganelle — Assembly of organelle genomes from whole-genome sequencing data
  • 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
  • GTDB-Tk — Taxonomic classification of bacterial and archaeal genomes using the GTDB

H

  • HADDOCK3 — High Ambiguity Driven biomolecular DOCKing
  • HeLI-OTS — Off-the-shelf language identifier with language models for 220 languages
  • HFST  — Helsinki Finite-State Transducer Technology
  • HFST-fi  — Helsinki Finite-State Technology for Finnish
  • HFST-sv  — Helsinki Finite-State Technology for Swedish
  • 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)

I

  • 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
  • Intel Trace Analyzer and Collector (ITAC) — MPI profiling and tracing tool
  • Intel VTune Profiler — Performance analysis tool for single core and threading performance
  • 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

J

  • 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
  • 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

K

  • kp-spell (enchant) — Finnish and Swedish spell-checking via the enchant interface
  • Kraken — Taxonomic sequence classification system
  • Krona visualization tool — Visualization tool for taxonomic classification and other hierarchical data

L

  • 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

M

  • 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
  • MaxQuant  — A proteomics software for processing of Mass-spectromtery data
  • medaka — Nanopore consensus and variant calling
  • Megahit — Metagenomics assembly
  • MEME Suite — Motif discovery and analysis (MEME Suite)
  • MetaBAT — Metagenome binning (MetaBAT2)
  • MetaPhlAn — Profiling the composition of microbial communities with metagenomic data
  • MICOM — Metabolic modelling of microbial communities
  • Minimap2 — Short read aligner
  • MIRA — Whole genome shotgun and EST sequence Assembler
  • 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)

N

  • 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
  • NMRLipids — NMRLipids databank containing MD simulations
  • nsys — Nvidia GPU and CPU profiler
  • nvprof — Nvidia profiling tool that collects and views profiling data
  • NWChem — A computational chemistry software package designed to perform well on parallel HPC systems

O

  • 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

P

  • PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows
  • PANNZER2/SANSPANZ — Automatic protein annotation tool
  • ParaView — Free open-source visualization application
  • PDAL — for point cloud translations and processing
  • pdb — Built-in Python debugger
  • Pennylane — Free open-source software framework for quantum machine learning and quantum computing
  • 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

Q

  • QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
  • QIIME — Package for microbial community analysis of amplicon sequencing 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

R

  • 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)
  • Roary — Pan genome pipeline
  • RStudio IDE — Integrated development environment for R
  • run_dbcan — Automated carbohydrate-active enzyme (CAZyme) annotation

S

  • 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
  • SameStr — Strain-level sharing analysis from metagenomic SNV profiles
  • SAMtools — Utilities for managing SAM/BAM formatted alignment files
  • Scalasca — Performance profiler for parallel programs
  • 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
  • Spark — High-performance distributed computing framework
  • SRA Toolkit — NCBI SRA Toolkit for accessing and converting SRA data
  • Stacks — Pipeline for building loci from short-read sequences (e.g. RAD-seq 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)

T

  • 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
  • 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

U

  • UDPipe — Trainable pipeline for tokenization, tagging, lemmatization and dependency parsing

V

  • VASP — Ab initio DFT electronic structures
  • VCFtools — VCF manipulation and statistics
  • Velvet — Genome assembler
  • VirusDetect — Virus identification with sRNA data
  • VisIt — Free open-source visualization application
  • Visual Studio Code — Source code editor
  • 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

W

  • Whisper — General-purpose speech recognition model
  • WhiteboxTools — an advanced geospatial data analysis platform
  • wtdbg2 — Fast assembler for long-read data

X

Z

  • Zonation — Spatial conservation prioritization framework