MetaCentrum Application List
Computational chemistry / Molecular modelling
Computational chemistry methods serve for computational simulations of real biological behaviour and chemical reactions and processes.
- ABINIT
- Amber
- Atomsk
- Autodock Vina
- Babel
- CCP4
- CP2K
- DALTON
- DBG2OLC
- DIRAC
- Gamess
- Gaussian-GaussView
- Gromacs
- LAMMPS
- Lobster
- Molden
- MolPro
- MOPAC
- NAMD
- ntJoin
- Newton-X
- NWChem
- OpenMolcas
- Orca
- PC GAMESS-Firefly
- Phenix
- Picard Tools
- Phonopy
- Smartflux (EddyPro)
- Serpent
- Superfold
- Tinker
- Turbomole
- VASP
Structural biology, biology and bioinformatics
Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules, especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures affect their function.
Aligners
- endhic
- allhic
- alignment
- Aliscore
- Bowtie
- BWA
- BWA-mem2
- ClustalOmega
- ClustalWX
- ERNE
- Exonerate
- FLASH
- Gemtools
- GMAP (GSNAP)
- Graphmap
- Hisat
- HMMER
- Last
- MAFFT
- Minimap
- Mstatx
- Mugsy
- MUMmer
- Muscle
- Novoalign2
- RapMap
- SeqTools
- SNAP
- SOAP
- SOAPalign
- Stampy
- Star
- Subread
- Tablet
- TopHat
- UMI-VarCal
- Wise
Annotation
- ACT
- Artemis
- autodock
- Blast
- Blast+
- Blat-suite
- CS-Rosetta
- Daccor
- dnaPipeTE
- edirect
- Fasta
- FPC
- Geneid
- Genoman
- GlimmerHMM
- HMMER
- Interproscan
- LiftOver
- LobSTR
- Ltrdigest
- Maker
- OMA
- RepeatMasker
- Rosetta
- snpEff
- Survivor
- Telomerecat
- Transrate
- Trinotate
- TRF
- VSEARCH
Assemblers
- ABySS
- Arcs
- Amos
- Canu
- Cap3-PCap
- Cicero
- Edena
- Flye
- HAPCUT2
- Haslr
- Irys
- KisSplice
- Masurca
- Meraculous
- Miniasm
- Mitobim
- Mira
- Mosaik
- Oases
- OPERA-MS
- Purge_dups
- Platanus
- quickmerge
- Rainbow
- Raven
- Ray
- SGA
- SOAPdenovo
- SOAPdenovo-trans
- SPAdes
- Supernova
- Tedna
- TransLiG
- Trinity
- Unicycler
- Velvet
- WGS
- 3D-DNA
Gene expression analysis
Metagenomics
Multipurpose bioinformatic packages
- Angsd
- Bedops
- CLCgenomicsWB
- Cufflinks
- Emboss
- Galaxy
- GenomeAnalysisTK (GATK)
- Geneious
- Genoman
- GenomeTools
- Hyphy
- LongRanger
- MEME Suite
- Mothur
- MP-EST
- Plink
- RNAframework
- TEtools
- UEA sRNA Workbench
Others
- Augustus
- Autogrow
- AYB
- BaitFisher
- Bayescan
- Bioperl
- Braker2
- BUSCO
- FreeBayes
- GeneMark
- GenomeThreader
- gibpss
- Guidance
- IMP
- jmodeltest2
- kma
- liftOver
- mapDamage2
- MCL
- Merqury
- Nextflow
- Omni-c
- Orthofinder
- Orthograph
- Preseq
- QUAST
- rMATS
- Rstudio
- Scan for matches
- SICER2
- Squat
- Strelka
- sniffles
- TADbit
- TelSeq
- Trim Galore!
- VelvetOptimiser
Phylogenetics
- ADMIXTURE
- ASTRAL
- BEAST
- BUCKy
- ChromEvol
- ETE
- ExaBayes
- ExaML
- FastTree
- GARLI
- Guenomu
- Hamstr
- IQ-TREE
- Jane
- Kraken2
- LDDist
- MP-EST
- MrBayes
- ModelTest-NG
- Newick Utilities
- PartitionFinder
- PAUP*
- Phycas
- PhyloBayes
- PhyML
- Phyparts
- Phyx
- R8s
- RAxML
- RAxML-NG
- raxmlGUI
- SNAPP
- SNPhylo
- stells2
- Structure
- TNT
- UBCG
Population genetics
Sequence data processing
- Bamtools
- Bam2fastq
- BAM2fastx_tools
- BamQC
- Bcftools
- Bcl2fastq2
- Bedtools
- CD-HIT
- CTK (CLIP Tool Kit)
- FastP
- FastQC
- Fastq Pair
- FastQValidator
- FASTQ_Illumina_Filter
- Fastx
- Flexbar
- HTSeq
- Jellyfish
- jvarkit
- KAT
- LINKS
- Medaka
- miRExpress
- NxTrim
- Nanopolish
- Nanopore sequencing - data analysis tools
- OCOCO
- ParDRe
- PEAR
- Picard Tools
- Piranha
- Porechop
- Preseq
- Prodigal
- QIIME
- Racon
- RepeatExplorer
- Repliscan
- Rins
- RSeQC
- Samblaster
- SAMtools
- Seqtk
- SLR
- Spladder
- SRA Toolkit
- Swarm
- Tassel
- TEPID
- Transdecoder
- TGICL
- Trimal
- Trimmomatic
- Ugene
- VCFtools
- Yaha
Sequence error correction
Visualisation
- CellProfiler
- Chimera
- Blobtools
- Clview
- DataAnalysis
- Edena
- FMRIB Software Library (FSL)
- Freesurfer
- GPAW
- LTRdigest
- Migrate
- Krona
- PyMOL
- SOLpro
- VASCo
- ViennaRNA
- VMD
- VTK
- X-PLOR
Technical and material simulations
MetaCentrum have available huge range of top-level programs from computational fluid dynamics, computational solid mechanics and associated disciplines.
- ANSYS with LS-DYNA module
- Basement
- Einstein Toolkit
- Espresso
- Fluent
- Meep
- MSC.Marc
- Neper
- Open Foam
- PALM
- PIConGPU
- UppASD
- WIEN2k
Mathematical and statistical modelling
The common standard mathematical and statistical packages are in MetaCentrum available as well, of course.
- CPLEX Optimizer
- Graph tool
- gridMathematica
- GSL – GNU Scientific Library
- Maple
- Mathematica
- Matlab
- NRG Ljubljana
- Octave
- R
- SageMath
Image, video and sound processing
Development tools and environments
Moreover, MetaCentrum offers also an access to professional development tools.
- .NET
- Apache Ant
- Apache Maven
- Caffe
- Cairo
- Cgal
- Conda - modules
- cuDNN library
- Debian-compat
- GCC
- GDAL
- Grace
- HDF5
- Intel CDK
- JDK
- Mono
- MZmine
- Numpy
- GNU Parallel
- PGI CDK
- PyPy
- Python
- Python - modules
- PyTorch
- Scientific Python
- Scipy
- SICStus Prolog
- SGI development environment
- TensorFlow library
- wxPython