Other bioinformatics programs
| Application purpose | Name | Short description | Links |
|---|---|---|---|
| SNP | freebayes | Bayesian haplotype-based genetic polymorphism discovery and genotyping. | homepage |
| kSNP | kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. | homepage | |
| VEP | Variant Effect Predictor predicts the functional effects of genomic variants. | homepage | |
| analysis | Beagle | software package for analysis of large-scale genetic data sets | homepage |
| DELLY2 | structural variant discovery by integrated paired-end and split-read analysis | publication, tutorial | |
| EMBOSS | analysis package for molecular biology (all programs are listed by command 'wossname', a detailed program description is displayed by 'tfm program_name') | homepage, tutorial | |
| GenomeTools | bioinformatics tools for genome analysis | homepage | |
| InterProScan | protein sequence search | homepage, publication | |
| MEME | supports motif-based analysis of DNA, RNA and protein sequences | homepage | |
| PLINK | whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner | homepage | |
| annotation | MAKER | genome annotation pipeline | homepage, publication |
| SnpEff | Genomic variant annotations and functional effect prediction toolbox. | homepage | |
| classification | Kraken2 | A 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-BLAST | basic local alignment search tool | homepage | |
| electron microscopy | ctffind | program for finding CTFs of electron micrographs | homepage |
| RELION | REgularised LIkelihood OptimisatioN: a program for an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy | tutorial | |
| Vlion | A slightly vectorized (AVX & SSE instructions) version of the original RELION 1.4 code. | homepage, tutorial | |
| gene prediction | AUGUSTUS | gene prediction program for eukaryotes | homepage |
| SNAP | Semi-HMM-based Nucleic Acid Parser: a gene prediction tool | homepage | |
| genome browser | Integrative Genomics Viewer | high-performance visualization tool for genomic datasets | homepage, publication |
| UCSC | genome browser | homepage | |
| genomics | AUGUSTUS | gene prediction program for eukaryotes | homepage |
| Beagle | software package for analysis of large-scale genetic data sets | homepage | |
| bedtools | toolset for genome arithmetic | homepage, tutorial | |
| CEAS | Cis-regulatory Element Annotation System for characterization of genome-wide protein-DNA interaction patterns from ChIP | homepage | |
| CNVnator | a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads | publication, tutorial | |
| DELLY2 | structural variant discovery by integrated paired-end and split-read analysis | publication, tutorial | |
| GenomeTools | bioinformatics tools for genome analysis | homepage | |
| Integrative Genomics Viewer | high-performance visualization tool for genomic datasets | homepage, publication | |
| MAKER | genome annotation pipeline | homepage, publication | |
| PLINK | whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner | homepage | |
| RECON | program for prediction of nucleosome formation potential | homepage, publication | |
| RepeatMasker | program that screens DNA sequences for interspersed repeats and low complexity DNA sequences | homepage | |
| SNAP | Semi-HMM-based Nucleic Acid Parser: a gene prediction tool | homepage | |
| Tabix | tool for fast retrieval of sequence features from generic TAB-delimited files | homepage, publication | |
| Tandem Repeats Finder | a program to locate and display tandem repeats in DNA sequences | homepage | |
| tRNAscan_SE | a program for improved detection of transfer RNA genes in genomic sequence | homepage, publication | |
| UCSC | genome browser | homepage | |
| metagenomics | Bracken | A 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 |
| Kraken2 | A 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 ecology | mothur | open-source expandable software for the bioinformatic needs of microbial ecology | homepage |
| MOTHUR-GUI | Gui version of mothur | homepage | |
| microscopy | PGURE-SVT | algorithm for denoising time-resolved microscopy image sequences | homepage, publication |
| multiple sequence alignment | Clustal W | command-line tool for multiple alignment of nucleic acid and protein sequences | homepage, tutorial |
| Clustal X | version of Clustal W with a GUI | homepage, tutorial | |
| MAFFT | multiple alignment program for amino acid or nucleotide sequences | homepage, publication | |
| Mauve | Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. | homepage, publication | |
| MUSCLE | multiple sequence alignment | homepage, publication | |
| SINA | tool for aligning sequences with an existing multiple sequence alignment (MSA) at high accuracy | homepage, publication | |
| T-Coffee | a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods | homepage | |
| phylogenetics | BEAST | Software package for phylogenetic analysis with an emphasis on time-scaled trees. | homepage |
| Beast2 | Bayesian Evolutionary Analysis by Sampling Trees (rewrite of BEAST) | homepage | |
| kSNP | kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. | homepage | |
| MrBayes | program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models | homepage | |
| PartitionFinder | select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses | homepage | |
| PHYLIP | PHYLogeny Inference Package: programs for inferring phylogenies | homepage | |
| PhyML | Phylogenetic estimation using (Maximum) Likelihood | homepage | |
| RAxML | Randomized Axelerated Maximum Likelihood: tool for maximum-likelihood based phylogenetic inference | homepage | |
| RAxML Next Generation | A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. | documentation, publication | |
| simRRLs | simulation of raw restriction-site associated DNA fastq files for testing assembly methods on raw data | homepage | |
| Structure | A software package for using multi-locus genotype data to investigate population structure. | homepage | |
| protein | InterProScan | protein sequence search | homepage, publication |
| PROFphd | Predicts protein secondary structure using a system of neural networks | homepage | |
| Proteome Discoverer | only usable as viewer on our server | homepage | |
| Rosetta | software suite including algorithms for computational modeling and analysis of protein structures | homepage | |
| SignalP | prediction of presence and location of signal peptide cleavage sites in amino acid sequences | homepage, publication | |
| sequence alignment | Clustal W | command-line tool for multiple alignment of nucleic acid and protein sequences | homepage, tutorial |
| Clustal X | version of Clustal W with a GUI | homepage, tutorial | |
| Exonerate | sequence alignment tool for pairwise sequence comparison | homepage | |
| FASTA | sequence comparison | homepage | |
| GMAP/GSNAP | GMAP: Genomic Mapping and Alignment Program for mRNA and EST Sequences. GSNAP: Genomic Short-read Nucleotide Alignment Program | homepage | |
| HMMER | biosequence analysis using profile hidden Markov models | homepage | |
| MAFFT | multiple alignment program for amino acid or nucleotide sequences | homepage, publication | |
| Mauve | Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. | homepage, publication | |
| MUMmer | a system for rapidly aligning entire genomes | homepage | |
| NCBI-BLAST | basic local alignment search tool | homepage | |
| SINA | tool for aligning sequences with an existing multiple sequence alignment (MSA) at high accuracy | homepage, publication | |
| T-Coffee | a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods | homepage | |
| single cell analysis | Monocle3 | Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments. | homepage |
| special purpose | CEAS | Cis-regulatory Element Annotation System for characterization of genome-wide protein-DNA interaction patterns from ChIP | homepage |
| CNVnator | a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads | publication, tutorial | |
| HMMER | biosequence analysis using profile hidden Markov models | homepage | |
| InterProScan | protein sequence search | homepage, publication | |
| MEME | supports motif-based analysis of DNA, RNA and protein sequences | homepage | |
| phASER | phasing and Allele Specific Expression from RNA-seq | homepage, publication | |
| RECON | program for prediction of nucleosome formation potential | homepage, publication | |
| RepeatMasker | program that screens DNA sequences for interspersed repeats and low complexity DNA sequences | homepage | |
| SignalP | prediction of presence and location of signal peptide cleavage sites in amino acid sequences | homepage, publication | |
| simRRLs | simulation of raw restriction-site associated DNA fastq files for testing assembly methods on raw data | homepage | |
| SRST2 | Short Read Sequence Typing for Bacterial Pathogens | homepage | |
| Tabix | tool for fast retrieval of sequence features from generic TAB-delimited files | homepage, publication | |
| Tandem Repeats Finder | a program to locate and display tandem repeats in DNA sequences | homepage | |
| Tomahawk | Fast calculations of linkage-disequilibrium in large-scale human cohorts | homepage | |
| tRNAscan_SE | a program for improved detection of transfer RNA genes in genomic sequence | homepage, publication | |
| statistics | Rgui | graphical user interface for R | homepage |
| Rstudio | A free and open-source environment for R, a programming language for statistical computing. Also available as RStudio-Server. | homepage | |
| structural biology | BUSTER | crystallographic structure refinement using Bayesian statistical methods | homepage, tutorial |
| DIALS | diffraction integration software for X-ray crystallography | homepage | |
| Gromacs | a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles | homepage | |
| iMOSFLM | a program for integrating single crystal diffraction data from area detectors | homepage | |
| PROFphd | Predicts protein secondary structure using a system of neural networks | homepage | |
| Rosetta | software suite including algorithms for computational modeling and analysis of protein structures | homepage | |
| Vienna RNA package | C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures | homepage | |
| toolkit | BioPerl | open source bioinformatics toolkit for writing bioinformatics scripts | homepage |
| EMBOSS | analysis package for molecular biology (all programs are listed by command 'wossname', a detailed program description is displayed by 'tfm program_name') | homepage, tutorial | |
| MEME | supports motif-based analysis of DNA, RNA and protein sequences | homepage | |
| PLINK | whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner | homepage | |
| utilities | bedtools | toolset for genome arithmetic | homepage, tutorial |
| biotools | Python package of bioinformatics utilities | homepage | |
| Entrez Direct | Entrez 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 | |
| Jellyfish | A tool for fast, memory-efficient counting of k-mers in DNA | homepage, tutorial | |
| KNIME | more than 1500 modules, hundreds of ready-to-run examples, community contributions, and tool integrations | homepage | |
| variants | DELLY2 | structural variant discovery by integrated paired-end and split-read analysis | publication, tutorial |
| freebayes | Bayesian haplotype-based genetic polymorphism discovery and genotyping. | homepage | |
| kSNP | kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. | homepage | |
| SnpEff | Genomic variant annotations and functional effect prediction toolbox. | homepage | |
| VEP | Variant Effect Predictor predicts the functional effects of genomic variants. | homepage | |
| visualization | Circos | software package for visualizing data and information in a circular layout | homepage |
| Integrative Genomics Viewer | high-performance visualization tool for genomic datasets | homepage, publication | |
| Miropeats | Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and presents this similarity information graphically. | homepage |
last modified: 14.05.2020 - 11:04