Other bioinformatics programs

Application purpose Name Short description Links
DNAAUGUSTUSgene prediction program for eukaryoteshomepage
Beaglesoftware package for analysis of large-scale genetic data setshomepage
bedtoolstoolset for genome arithmetichomepage, tutorial
CEASCis-regulatory Element Annotation System for characterization of genome-wide protein-DNA interaction patterns from ChIPhomepage
CNVnatora tool for CNV discovery and genotyping from depth-of-coverage by mapped readspublication, tutorial
DELLY2structural variant discovery by integrated paired-end and split-read analysispublication, tutorial
Exoneratesequence alignment tool for pairwise sequence comparisonhomepage
freebayesBayesian haplotype-based genetic polymorphism discovery and genotyping.homepage
GenomeToolsbioinformatics tools for genome analysishomepage
HMMERbiosequence analysis using profile hidden Markov modelshomepage
Integrative Genomics Viewerhigh-performance visualization tool for genomic datasetshomepage, publication
JellyfishA tool for fast, memory-efficient counting of k-mers in DNAhomepage, tutorial
MAKERgenome annotation pipelinehomepage, publication
MauveMauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.homepage, publication
MiropeatsMiropeats discovers regions of sequence similarity amongst any set of DNA sequences and presents this similarity information graphically.homepage
PHYLIPPHYLogeny Inference Package: programs for inferring phylogenieshomepage
PLINKwhole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient mannerhomepage
RAxMLRandomized Axelerated Maximum Likelihood: tool for maximum-likelihood based phylogenetic inferencehomepage
RECONprogram for prediction of nucleosome formation potentialhomepage, publication
RepeatMaskerprogram that screens DNA sequences for interspersed repeats and low complexity DNA sequenceshomepage
SNAPSemi-HMM-based Nucleic Acid Parser: a gene prediction toolhomepage
Tabixtool for fast retrieval of sequence features from generic TAB-delimited fileshomepage, publication
Tandem Repeats Findera program to locate and display tandem repeats in DNA sequenceshomepage
tRNAscan_SEa program for improved detection of transfer RNA genes in genomic sequencehomepage, publication
VEPVariant Effect Predictor predicts the functional effects of genomic variants.homepage
RNAphASERphasing and Allele Specific Expression from RNA-seqHomepage, publication
SINAtool for aligning sequences with an existing multiple sequence alignment (MSA) at high accuracyhomepage, publication
VEPVariant Effect Predictor predicts the functional effects of genomic variants.homepage
Vienna RNA packageC code library and several stand-alone programs for the prediction and comparison of RNA secondary structureshomepage
SNPfreebayesBayesian haplotype-based genetic polymorphism discovery and genotyping.homepage
kSNPkSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.homepage
VEPVariant Effect Predictor predicts the functional effects of genomic variants.homepage
analysisBeaglesoftware package for analysis of large-scale genetic data setshomepage
DELLY2structural variant discovery by integrated paired-end and split-read analysispublication, tutorial
EMBOSSanalysis package for molecular biology (all programs are listed by command 'wossname', a detailed program description is displayed by 'tfm program_name')homepage, tutorial
GenomeToolsbioinformatics tools for genome analysishomepage
InterProScanprotein sequence searchhomepage, publication
MEMEsupports motif-based analysis of DNA, RNA and protein sequenceshomepage
PLINKwhole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient mannerhomepage
annotationMAKERgenome annotation pipelinehomepage, publication
classificationKraken2A taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. The assisting tool Bracken is available in a separate module.homepage
NCBI-BLASTbasic local alignment search toolhomepage
electron microscopyctffindprogram for finding CTFs of electron micrographshomepage
RELIONREgularised LIkelihood OptimisatioN: a program for an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopytutorial
VlionA slightly vectorized (AVX & SSE instructions) version of the original RELION 1.4 code.homepage, tutorial
gene predictionAUGUSTUSgene prediction program for eukaryoteshomepage
SNAPSemi-HMM-based Nucleic Acid Parser: a gene prediction toolhomepage
genome browserUCSCgenome browserhomepage
genomicsAUGUSTUSgene prediction program for eukaryoteshomepage
Beaglesoftware package for analysis of large-scale genetic data setshomepage
bedtoolstoolset for genome arithmetichomepage, tutorial
CEASCis-regulatory Element Annotation System for characterization of genome-wide protein-DNA interaction patterns from ChIPhomepage
CNVnatora tool for CNV discovery and genotyping from depth-of-coverage by mapped readspublication, tutorial
DELLY2structural variant discovery by integrated paired-end and split-read analysispublication, tutorial
GenomeToolsbioinformatics tools for genome analysishomepage
Integrative Genomics Viewerhigh-performance visualization tool for genomic datasetshomepage, publication
MAKERgenome annotation pipelinehomepage, publication
PLINKwhole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient mannerhomepage
RECONprogram for prediction of nucleosome formation potentialhomepage, publication
RepeatMaskerprogram that screens DNA sequences for interspersed repeats and low complexity DNA sequenceshomepage
SNAPSemi-HMM-based Nucleic Acid Parser: a gene prediction toolhomepage
Tabixtool for fast retrieval of sequence features from generic TAB-delimited fileshomepage, publication
Tandem Repeats Findera program to locate and display tandem repeats in DNA sequenceshomepage
tRNAscan_SEa program for improved detection of transfer RNA genes in genomic sequencehomepage, publication
UCSCgenome browserhomepage
metagenomicsBrackenA highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses taxonomy labels assigned by Kraken/Kraken2.homepage
Kraken2A taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. The assisting tool Bracken is available in a separate module.homepage
microbial ecologymothuropen-source expandable software for the bioinformatic needs of microbial ecologyhomepage
MOTHUR-GUIGui version of mothurhomepage
microscopyPGURE-SVTalgorithm for denoising time-resolved microscopy image sequenceshomepage, publication
multiple sequence alignmentClustal Wcommand-line tool for multiple alignment of nucleic acid and protein sequenceshomepage, tutorial
Clustal Xversion of Clustal W with a GUIhomepage, tutorial
MAFFTmultiple alignment program for amino acid or nucleotide sequenceshomepage, publication
MauveMauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.homepage, publication
MUSCLEmultiple sequence alignmenthomepage, publication
SINAtool for aligning sequences with an existing multiple sequence alignment (MSA) at high accuracyhomepage, publication
T-Coffeea multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methodshomepage
phylogeneticsBEASTBayesian analysis for molecular sequenceshomepage
kSNPkSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.homepage
MrBayesprogram for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary modelshomepage
PartitionFinderselect best-fit partitioning schemes and models of molecular evolution for phylogenetic analyseshomepage
PHYLIPPHYLogeny Inference Package: programs for inferring phylogenieshomepage
RAxMLRandomized Axelerated Maximum Likelihood: tool for maximum-likelihood based phylogenetic inferencehomepage
simRRLssimulation of raw restriction-site associated DNA fastq files for testing assembly methods on raw datahomepage
StructureA software package for using multi-locus genotype data to investigate population structure.homepage
proteinInterProScanprotein sequence searchhomepage, publication
PROFphdPredicts protein secondary structure using a system of neural networkshomepage
Proteome Discovereronly usable as viewer on our serverhomepage
Rosettasoftware suite including algorithms for computational modeling and analysis of protein structureshomepage
SignalPprediction of presence and location of signal peptide cleavage sites in amino acid sequenceshomepage, publication
sequence alignmentClustal Wcommand-line tool for multiple alignment of nucleic acid and protein sequenceshomepage, tutorial
Clustal Xversion of Clustal W with a GUIhomepage, tutorial
Exoneratesequence alignment tool for pairwise sequence comparisonhomepage
FASTAsequence comparisonhomepage
HMMERbiosequence analysis using profile hidden Markov modelshomepage
MAFFTmultiple alignment program for amino acid or nucleotide sequenceshomepage, publication
MauveMauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.homepage, publication
MUMmera system for rapidly aligning entire genomeshomepage
NCBI-BLASTbasic local alignment search toolhomepage
SAMtoolsvarious utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position formathomepage
SINAtool for aligning sequences with an existing multiple sequence alignment (MSA) at high accuracyhomepage, publication
T-Coffeea multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methodshomepage
sequence comparisonExoneratesequence alignment tool for pairwise sequence comparisonhomepage
FASTAsequence comparisonhomepage
special purposeCEASCis-regulatory Element Annotation System for characterization of genome-wide protein-DNA interaction patterns from ChIPhomepage
CNVnatora tool for CNV discovery and genotyping from depth-of-coverage by mapped readspublication, tutorial
HMMERbiosequence analysis using profile hidden Markov modelshomepage
InterProScanprotein sequence searchhomepage, publication
MEMEsupports motif-based analysis of DNA, RNA and protein sequenceshomepage
RECONprogram for prediction of nucleosome formation potentialhomepage, publication
RepeatMaskerprogram that screens DNA sequences for interspersed repeats and low complexity DNA sequenceshomepage
SignalPprediction of presence and location of signal peptide cleavage sites in amino acid sequenceshomepage, publication
simRRLssimulation of raw restriction-site associated DNA fastq files for testing assembly methods on raw datahomepage
SRST2Short Read Sequence Typing for Bacterial Pathogenshomepage
Tabixtool for fast retrieval of sequence features from generic TAB-delimited fileshomepage, publication
Tandem Repeats Findera program to locate and display tandem repeats in DNA sequenceshomepage
tRNAscan_SEa program for improved detection of transfer RNA genes in genomic sequencehomepage, publication
statisticsRguigraphical user interface for R homepage
RstudioA free and open-source environment for R, a programming language for statistical computing. Also available as RStudio-Server.homepage
structural biologyBUSTERcrystallographic structure refinement using Bayesian statistical methodshomepage, tutorial
DIALSdiffraction integration software for X-ray crystallographyhomepage
Gromacsa versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particleshomepage
iMOSFLMa program for integrating single crystal diffraction data from area detectorshomepage
PROFphdPredicts protein secondary structure using a system of neural networkshomepage
Rosettasoftware suite including algorithms for computational modeling and analysis of protein structureshomepage
Vienna RNA packageC code library and several stand-alone programs for the prediction and comparison of RNA secondary structureshomepage
toolkitBioPerlopen source bioinformatics toolkit for writing bioinformatics scriptshomepage
EMBOSSanalysis package for molecular biology (all programs are listed by command 'wossname', a detailed program description is displayed by 'tfm program_name')homepage, tutorial
MEMEsupports motif-based analysis of DNA, RNA and protein sequenceshomepage
PLINKwhole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient mannerhomepage
utilitiesbedtoolstoolset for genome arithmetichomepage, tutorial
biotoolsPython package of bioinformatics utilitieshomepage
Entrez DirectEntrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.homepage
JellyfishA tool for fast, memory-efficient counting of k-mers in DNAhomepage, tutorial
KNIMEmore than 1500 modules, hundreds of ready-to-run examples, community contributions, and tool integrationshomepage
SAMtoolsvarious utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position formathomepage
variantsDELLY2structural variant discovery by integrated paired-end and split-read analysispublication, tutorial
freebayesBayesian haplotype-based genetic polymorphism discovery and genotyping.homepage
kSNPkSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.homepage
VEPVariant Effect Predictor predicts the functional effects of genomic variants.homepage
visualizationCircossoftware package for visualizing data and information in a circular layouthomepage
Integrative Genomics Viewerhigh-performance visualization tool for genomic datasetshomepage, publication
MiropeatsMiropeats discovers regions of sequence similarity amongst any set of DNA sequences and presents this similarity information graphically.homepage

last modified: 18.07.2019 - 11:48