Applications by discipline

Note

In addition to technical support, CSC also provides expert consulting in questions related to sciences and methods. For more details, see our science-specific support pages at research.csc.fi or directly contact our Service Desk .

Biosciences

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
Alphafold — Protein 3D structure prediction
ANGSD — Analysis of next-generation sequencing data via genotype likelihoods
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
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
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
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
CLUMPP — Alignment of replicate cluster assignments from population-structure analyses
Clustal Omega — Multiple sequence alignment
ClustalW — Multiple sequence alignment
CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
Cufflinks — Transcript assembly and differential expression for RNA-Seq
Cutadapt — Trimming high-throughput sequencing reads
deepTools — Tools for exploring deep-sequencing coverage data
Diamond — Sequence similarity search tool for proteins and nucleotides
Dorado — GPU-accelerated Oxford Nanopore basecaller
eggNOG-mapper — Functional annotation of sequences via orthology (eggNOG)
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
Freebayes — Genetic variant detector
gapseq — Genome-scale metabolic network reconstruction and analysis
GATK — Genome Analysis Toolkit for variant discovery
GetOrganelle — Assembly of organelle genomes from whole-genome sequencing data
GOLD — Protein Ligand Docking Software
Grace — Plotting tool for xvg-files in particular
GROMACS — Fast and versatile classical molecular dynamics
GTDB-Tk — Taxonomic classification of bacterial and archaeal genomes using the GTDB
HADDOCK3 — High Ambiguity Driven biomolecular DOCKing
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
HyPhy — Hypothesis testing on phylogenies (selection analysis)
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
Jellyfish — Fast k-mer counting
Kraken — Taxonomic sequence classification system
Krona visualization tool — Visualization tool for taxonomic classification and other hierarchical data
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)
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
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)
NCBI C++ Toolkit — NCBI C++ Toolkit libraries and command-line applications
Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
PANNZER2/SANSPANZ — Automatic protein annotation tool
PHYLIP — PHYLIP phylogeny inference package
Picard Tools — Tools for working with SAM,BAM,CRAM and VCF files
Prodigal — Prokaryotic gene prediction
Prokka — Rapid prokaryotic genome annotation
QIIME — Package for microbial community analysis of amplicon sequencing data
RAxML — Program for inferring phylogenies with likelihood
RAxML-NG — Maximum-likelihood phylogenetic inference (RAxML-NG)
Roary — Pan genome pipeline
run_dbcan — Automated carbohydrate-active enzyme (CAZyme) annotation
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
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
Stacks — Pipeline for building loci from short-read sequences (e.g. RAD-seq data)
STAR — Short read aligner
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)
TopHat — Splice junction mapper for RNA-Seq reads
Trimmomatic — Trim Illumina paired-end and single-read data
Trinity — Transcriptome assembly tool
VCFtools — VCF manipulation and statistics
Velvet — Genome assembler
VirusDetect — Virus identification with sRNA data
VMD — Molecular visualization program
VSEARCH — Versatile sequence search and clustering
wtdbg2 — Fast assembler for long-read data
XHMM (eXome-Hidden Markov Model) — Copy number variation calling from targeted sequencing data

Chemistry

Amber — Molecular dynamics suite
AMS — Modelling suite providing the ADF engine
AMS-GUI — AMS integrated GUI
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
CSD — Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools
Gaussian — Versatile computational chemistry package
GOLD — Protein Ligand Docking Software
GPAW — Versatile DFT package
GROMACS — Fast and versatile classical molecular dynamics
HADDOCK3 — High Ambiguity Driven biomolecular DOCKing
LAMMPS — Fast molecular dynamics engine with large force field selection
Maestro — Versatile drug discovery and materials modeling suite
Molden — Processing program for molecular and electronic structure calculations
MOLPRO — Package for accurate ab initio quantum chemistry calculations
NAMD — Highly scalable classical molecular dynamics
NMRLipids — NMRLipids databank containing MD simulations
NWChem — A computational chemistry software package designed to perform well on parallel HPC systems
Open Babel — Program to interconvert file formats currently used in molecular modeling
ORCA — General-purpose quantum chemistry package
PLUMED — Library and tools for enhanced sampling methods
Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale
TmoleX — GUI for setting up and analyzing TURBOMOLE jobs
TURBOMOLE — Fast and robust quantum chemistry program package
VASP — Ab initio DFT electronic structures
VMD — Molecular visualization program

Computational Engineering

Abaqus — Dassault Systemes' SIMULIA academic research suite
Ansys — Ansys Academic research CFD
COMSOL Multiphysics — General-purpose simulation software
Elmer — Open source multi-physics FEM package
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
Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software

Data Analytics and Machine Learning

JAX — Autograd and XLA, brought together for high-performance machine learning
Python Data — Collection of Python libraries for data analytics and machine learning
PyTorch — Machine learning framework for Python
Spark — High-performance distributed computing framework
TensorFlow — Deep learning library for Python
vLLM — A fast and easy-to-use library for LLM inference and serving
Whisper — General-purpose speech recognition model

Geosciences

ArcGIS Python API — Spatial analysis and data science
CloudCompare — for visualizing, editing and processing point clouds
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
LAStools — for LiDAR datasets
OpenDroneMap (ODM) — for processing aerial drone imagery
Orfeo ToolBox — for remote sensing applications
PDAL — for point cloud translations and processing
Python-geo — Python libraries for spatial analysis
QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
R for GIS — R spatial analysis libraries
SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
SNAP — for remote sensing applications
WhiteboxTools — an advanced geospatial data analysis platform
Zonation — Spatial conservation prioritization framework

eBay's tsv-utils — Utilities for manipulating large tabular data files
Finnish Tagtools — Finnish Tagtools
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
kp-spell (enchant) — Finnish and Swedish spell-checking via the enchant interface
openSMILE — Toolkit for extracting audio features for speech and music analysis
Praat — Toolkit for annotating, processing and analysing speech and other audio samples
trankit — Transformer-based Python toolkit for multilingual Natural Language Processing (NLP)
UDPipe — Trainable pipeline for tokenization, tagging, lemmatization and dependency parsing
vrt-tools — Tools for converting VRT (Vertical Text) corpus files

Mathematics and Statistics

IDL — Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
Julia Language — High-level, high-performance dynamic programming language for numerical computing
MATLAB — High-level technical computing language
Octave — High-level interpreted language for numerical computations
Python — The programming language and its modules at CSC
r-env — R and RStudio Server
RStudio IDE — Integrated development environment for R
SageMath — Free open-source mathematics software system

Physics

VASP — Ab initio DFT electronic structures

Quantum

Cirq-on-iqm — open-source cirq adapter for quantum computing
Pennylane — Free open-source software framework for quantum machine learning and quantum computing
Qiskit — open-source toolkit for useful quantum computing
Qiskit-on-iqm — open-source qiskit adapter for quantum computing

Atmosphere research

CDO — Command line tools to manipulate and analyse Climate and NWP model Data

Miscellaneous

Accelerated visualization — A selection of GPU accelerated visualization applications
Blender — 3D modeling, visualization and rendering software
compute-sanitizer — Functional correctness checking suite included in the CUDA toolkit
cProfile — Built-in profiler for Python programs
cuda-gdb — Nvidia extension of the GNU debugger GDB
DDT — Parallel debugger
Desktop — Remote desktop environment
FFmpeg — Tools and libraries for recording, converting and streaming audio and video
FireWorks — FireWorks is a free, open-source tool for defining, managing and executing workflows with multiple steps and complex dependencies
gdb — GNU debugger for compiled programs
HyperQueue — Scheduler for sub-node tasks
Intel Trace Analyzer and Collector (ITAC) — MPI profiling and tracing tool
Intel VTune Profiler — Performance analysis tool for single core and threading performance
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
ncu — Nvidia CUDA kernel profiler
nsys — Nvidia GPU and CPU profiler
nvprof — Nvidia profiling tool that collects and views profiling data
ParaView — Free open-source visualization application
pdb — Built-in Python debugger
perf — Command line tool for performance analysis
Scalasca — Performance profiler for parallel programs
TensorBoard — The visualization toolkit for TensorFlow
VisIt — Free open-source visualization application
Visual Studio Code — Source code editor