biology
Bioinformatics and biology research tools
250 packages
PackageDescriptionSizeVersionRdeps
abyssAssembly By Short Sequences: parallel, paired-end sequence assembler7.02MiB2.3.10ad2vcfAdd allelic depth info from a SAM stream to a VCF file22.9KiB0.1.6.191andiEfficient estimation of evolutionary distances517KiB0.14.3artemisDNA sequence viewer and annotation tool110MiB17.0.1.11atac-seqMetaport for ATAC-Seq analysis243B0.2.0_1augustus-gene-predictionGenome annotation tool155MiB3.5.0_16avidaAuto-adaptive genetic system designed for ALife research11.6MiB2.12.4babelConverts among various molecular file formats337KiB1.6_4bamtoolsAPI and toolkit for handling BAM files1.07MiB2.5.33bamutilUtilities for working with SAM/BAM files961KiB1.0.151barrnapBAsic Rapid Ribosomal RNA Predictor3.04MiB0.9bbmapBBMap short read aligner, and other bioinformatic tools28.8MiB39.341bcf-scoreBcftools plugins for GWAS-VCF summary statistics files349KiB1.20_3bcftoolsTools for manipulating next-generation sequencing data2.60MiB1.225bedtoolsToolset for genome set arithmetic such as intersect, union1.58MiB2.31.15bfcCorrect sequencing errors from Illumina sequencing data56.5KiBg201504171bifrostParallel construction, indexing and querying of de Bruijn graphs6.07MiB1.3.5_1bio-mochaBcftools plugin for mosaic chromosomal alteration analysis273KiB1.20_11bioawkBWK awk modified for biological data212KiB1.0.71biococoaBioinformatics framework766KiB2.2.2_91biolibcLow-level high-performance bioinformatics library557KiB0.2.77biolibc-toolsHigh-performance bioinformatics tools based on biolibc108KiB0.1.53bioparserC++ header-only parsing library for several formats in bioinformatics32.7KiB3.1.0biosigLibrary for reading and writing different biosignal data format6.75MiB2.6.1_23biosoupCollection of C++ header-only data structures for bioinformatics22.3KiB0.11.0_11biostar-toolsMeta-port for Biostar Handbook tools1.04KiB2.1bolt-lmmMixed model association testing and variance component analysis319MiB2.3.6_17bowtieUltrafast, memory-efficient short read aligner14.8MiB1.3.1bowtie2Ultrafast, memory-efficient short read aligner24.2MiB2.5.43btllibBioinformatics Technology Lab common code library2.42MiB1.7.5_11bwaBurrows-Wheeler sequence aligner404KiB0.7.194canuSingle molecule sequence assembler10.6MiB2.2_8cd-hitClustering and comparing protein or nucleotide sequences958KiB4.8.1_33cdbfastaFast indexing and retrieval of FASTA records from flat file databases193KiB2023.07.10chip-seqMetaport for ChIP-Seq analysis243B0.1.2_1clustal-omegaMultiple alignment of nucleic acid and protein, replaces clustalw2.11MiB1.2.41clustalwMultiple alignment program for DNA or proteins704KiB2.1_31covermRead coverage calculator for metagenomics4.79MiB0.7.0_11cufflinksCufflinks assembles transcripts, estimates their abundance, etc9.61MiB2.2.1.89_13cytoscapeSoftware to visualize molecular interaction networks, gene expression1.23GiB3.6.1dDocentBash pipeline for RAD sequencing177KiB2.7.8_2diamondBLAST-compatible local sequence aligner6.37MiB2.1.16dsr-pdbSimple C++ PDB reader (reads the protein description format)1.65MiB1.0.3_17edlibFast C++ library for sequence alignment using edit distance47.5KiB1.2.7embossCollection of open source tools for genetic sequence analysis501MiB6.6.0_71erminejAnalyses of gene sets such as gene expression profiling studies15.3MiB3.21exonerateGeneric tool for sequence alignment6.87MiB2.4.0_1fasdaFast and simple differential analysis111KiB0.2.0.13fasda-utilsFast and simple differential analysis extras7.05KiB0.1.0.2_1fastaCollection of programs for searching DNA and protein databases496KiB21.1.1_1fasta3Collection of programs for searching DNA and protein databases5.77MiB36.3.8_1fastahackUtility for indexing and sequence extraction from FASTA files239KiB1.0.0fastaniFast Whole-Genome Similarity (ANI) Estimation306KiB1.34fastdnamlFaster DNAML, makes phylogenetic trees using maximum likelihood145KiB1.2.2_2fastoolSimple and quick FastQ and FastA tool for file reading and conversion12.7KiB0.1.4fastpUltra-fast all-in-one FASTQ preprocessor551KiB0.26.01fastq-trimLightening fast sequence read trimmer89.1KiB0.1.43fastqcQuality control tool for high throughput sequence data11.9MiB0.12.15FastTreeApproximately-maximum-likelihood phylogenetic trees from alignments237KiB2.1.11fastx_toolkitCLI tools for Short-Reads FASTA/FASTQ files preprocessing371KiB0.0.14_1fermi-liteLibrary and tool for assembling Illumina short reads in small regions514KiB0.1.13_21figtreeGraphical viewer of phylogenetic trees4.46MiB1.4.4.14flashFast Length Adjustment of SHort reads111KiB1.2.111fluctuateProgram to fit population models152KiB1.40freebayesBayesian haplotype-based polymorphism discovery and genotyping2.96MiB1.3.92garlicMolecular viewer, editor, and visualization program2.28MiB1.6_1gatkGenome Analysis Toolkit406MiB4.6.2.0gctaGenome-wide Complex Trait Analysis3.79MiB1.94.1_3gemmaGenome-wide Efficient Mixed Model Association59.3MiB0.98.5_1generandGenerate random genomic data in FASTA/FASTQ, SAM, or VCF format12.9KiB0.1.2_1gff2psConvert gff-formatted genomic data sets to PostScript788KiB0.98lgffreadGFF/GTF format conversions, filtering, FASTA extraction, etc282KiB0.12.72gklAccelerated kernel library for genomics281KiB0.9.11gmapGenomic Mapping and Alignment Program for mRNA and EST Sequences38.9MiB2020.09.12gperiodicDisplays a periodic table of the elements866KiB3.0.3_1graphlanHigh-quality circular representations of taxonomic, phylogenetic trees289KiB1.1.3_1GroopMMetagenomic binning suite1.79MiB0.3.4_6haplohseqIdentify regions of allelic imbalance60.3MiB0.1.2.3_21hhsuiteRemote protein homology detection suite115MiB3.3.0_3hisat2Alignment program for mapping next-generation sequencing reads4.65MiB2.2.1_22hmmerProfile hidden Markov models for biological sequence analysis13.9MiB3.41htslibC library for high-throughput sequencing data formats7.05MiB1.2217hyphyHypothesis testing using Phylogenies6.68MiB2.5.90igvVisualization tool for genomic datasets60.8MiB2.16.0_11infernalSearch sequence databases for structural RNA homologs25.1MiB1.1.51io_libGeneral purpose trace file (and Experiment File) reading interface2.35MiB1.14.10_11iqtreeEfficient phylogenomic software by maximum likelihood13.7MiB3.0.1jalviewViewer and editor for multiple sequence alignments44.5MiB2.11.2.5JellyfishFast, memory-efficient counting of k-mers in DNA1.14MiB2.3.0_41kallistoQuantify abundances of transcripts from RNA-Seq data2.28MiB0.51.1_1,12kmcpAccurate metagenomic profiling & fast large-scale genome searching11.2MiB0.9.4_22lamarcPackage of programs for computing population parameters7.49MiB2.1.8_2,1libbigwigC library for handling bigWig files (containing genomic data)99.6KiB0.4.8libcombineC++ library for working with the COMBINE archive format1.94MiB0.2.20_1libgffGFF/GTF parsing library based on GCLib548KiB2.0.0libgtextutilsGordon's text utilities76.9KiB0.71libneurosimCommon interfaces for neuronal simulators302KiB1.2.0_1libnumlC++ library for Numerical Markup Language5.50MiB1.1.7_13libsbmlAPI Library for Working with SBML File32.1MiB5.20.5_14libsedmlC++ SED-ML library13.5MiB2.0.33_11locarnaLocARNA provides several tools for the structural analysis of RNA25.9MiB2.0.0_1mafftMultiple alignment program for amino acid or nucleotide sequences10.0MiB7.267_11mapm3Constructs linkage maps of markers segregating in experimental crosses861KiB3.0_1mashmapFast approximate aligner for long DNA sequences657KiB3.1.3mca-callingCore tools for Mosaic Chromosomal Alteration event calling243B0.1.0megahitUltra-fast single-node large and complex metagenomics assembly4.18MiB1.2.9.20metaeukGene discovery and annotation for large-scale eukaryotic metagenomics11.5MiB7migrateProgram to estimate population sizes and migration rates3.83MiB5.0.6_2minimap2Pairwise aligner for genomic and spliced nucleotide sequences494KiB2.301MMseqs2Ultra fast and sensitive sequence search and clustering suite10.9MiB17.b804.fmoldenDisplay molecular orbitals and electron densities in 2D and 3D19.2MiB7.1_1,1mothurSoftware for bioinformatics of the microbial ecology community17.3MiB1.48.2mrbayesBayesian inference of phylogeny7.21MiB3.2.7_2mummerModular system for rapid whole genome alignment1.89MiB4.0.11muscleMUltiple Sequence Comparison by Log-Expectation389KiB3.8.1551ncbi-blast+NCBI implementation of Basic Local Alignment Search Tool930MiB2.17.01ncbi-cxx-toolkitNCBI C++ Toolkit193MiB29.7.0ncbi-entrez-directAccess to the NCBI's suite of interconnected databases10.7MiB14.9.20210423_381ncbi-toolkitNCBI development toolkit, including BLAST 2 and GenBank/Entrez support588MiB2017.01.06_9ngs-sdkTools and libraries for using data in the INSDC Sequence Read Archives826KiB3.0.1p5-AcePerlPerl5 interface to the ACEDB genome database system681KiB1.92_5p5-Bio-ASN1-EntrezGeneRegular expression-based Perl Parser for NCBI Entrez Gene149KiB1.73_2,11p5-Bio-ClusterBioPerl cluster modules162KiB1.7.3_12p5-Bio-CoordinateModules for working with biological coordinates179KiB1.0070011p5-Bio-DasClient-side library for Distributed Genome Annotation System305KiB1.17_4p5-Bio-Das-LitePerl extension for the DAS (HTTP+XML) Protocol58.2KiB2.11_1p5-Bio-DB-EMBLDatabase object interface for EMBL entry retrieval43.4KiB1.7.4p5-Bio-DB-NCBIHelperCollection of routines useful for queries to NCBI databases145KiB1.7.8p5-Bio-FeatureIOHandler for FeatureIO160KiB1.6.9051p5-Bio-GFF3Fast low-level functions for parsing and formatting GFF351.4KiB2.0_2p5-Bio-GlitePerl Interface to G-language35.3KiB0.10_2p5-Bio-GraphicsGenerate GD Images of Bio::Seq Objects1.49MiB2.40_2p5-Bio-MAGETABData model and utility API for the MAGE-TAB format580KiB1.31_2p5-Bio-NEXUSObject-oriented Perl API for the NEXUS file format553KiB0.78_1p5-Bio-PhyloPhylogenetic analysis using Perl1.66MiB2.0.1p5-Bio-SCFRead and Update SCF Chromatographic Sequence Files45.3KiB1.03_21p5-Bio-VariationBioPerl variation-related functionality236KiB1.7.51p5-BioPerlCollection of Perl modules for bioinformatics8.29MiB1.00700811p5-BioPerl-RunWrapper modules for common bioinformatics tools1.66MiB1.007003p5-transdecoderIdentify candidate coding regions within transcript sequences462KiB5.7.1p5-TrimGaloreWrapper around Cutadapt and FastQC for adapter and quality trimming24.8MiB0.6.10pamlPhylogenetic Analysis by Maximum Likelihood (PAML)13.3MiB4.10.9pbbamPacBio BAM C++ library, with SWIG bindings2.70MiB0.18.0_13peak-classifierClassify ChIP/ATAC-Seq peaks based on features provided in a GFF32.1KiB0.1.4.13_22pear-mergerMemory-efficient and highly accurate paired-end read merger686KiB0.9.6_11phymlSimple, fast, and accurate algorithm to estimate large phylogenies1.71MiB3.3.20220408_1,1picard-toolsCLI tools for manipulating high-throughput sequencing (HTS) data16.7MiB2.22.91plinkWhole genome association analysis toolset1.99MiB1.90.b6.17_5poolerOptimise DNA sequencing primer-set combinations163KiB1.89preseqPredict yield of distinct reads from a genomic library1.50MiB3.2.0primer3Primer3 helps to choose primers for PCR reactions267KiB2.3.6prodigalProtein-coding gene prediction for prokaryotic genomes26.8MiB2.6.3.16prodigy-ligPrediction of protein-small molecule binding affinities107KiB1.1.3_1protomolOO, component based, framework for molecular dynamics (MD) simulations12.7MiB2.0.3_16psi88Plotting wavefunctions (molecular orbitals) in 3D207KiB1.0_17py311-bcbio-gffRead and write Generic Feature Format (GFF) with Biopython integration183KiB0.7.1_11py311-biom-formatBiological Observation Matrix (BIOM) Format Project51.5MiB2.1.16_11py311-biopythonCollection of Python modules for bioinformatics25.2MiB1.85_24py311-biosigLibrary for reading and writing different biosignal data format45.0KiB2.6.1_1py311-bx-pythonPython module for reading, manipulating and writing genomic data sets4.39MiB0.14.01py311-crossmapLift over genomics coordinates between assemblies523KiB0.7.3_11py311-cutadaptTrim adapters from high-throughput sequencing reads1.33MiB5.22py311-deepToolsUser-friendly tools for exploring deep-sequencing data2.42MiB3.5.2_21py311-deeptoolsintervalsPython interface for deepTools interval trees310KiB0.1.9_11py311-dna-features-viewerPython library to visualize DNA features, e.g. GenBank or Gff files288KiB3.1.3_2py311-dnaioRead and write FASTQ and FASTA419KiB1.2.41py311-ete3Framework for the analysis and visualization of trees13.6MiB3.1.3_3py311-Genesis-PyAPIAPI for the Genesis platform for genetics information processing97.8KiB1.2.1_1py311-gffutilsWork with GFF and GTF files in a flexible database framework10.2MiB0.13_1py311-goatoolsTools for processing and visualizing Gene Ontology terms333MiB1.1.6_21py311-gtfparseParsing tools for GTF (gene transfer format) files84.4KiB2.5.0_1py311-hitsUtilities for processing high-throughput sequencing experiments4.29MiB0.1_1py311-HTSeqPython library to facilitate programmatic analysis of sequence data1.36MiB2.0.9_2py311-libnumlNumerical Markup Language for Python1.22MiB1.1.7py311-libsedmlSED-ML library for Python3.75MiB2.0.33py311-loompyWork with .loom files for single-cell RNA-seq data697KiB3.0.7_2py311-macs2Identify transcription factor binding sites3.67MiB2.2.9.1_12py311-MACS3Peak caller aimed at transcription factor binding sites7.82MiB3.0.3py311-mrcfileMRC file I/O library which is used in structural biology421KiB1.5.3_11py311-multiqcAggregate bioinformatics analysis reports across samples and tools23.0MiB1.25.2_34py311-newickPython module to read and write the Newick format136KiB1.10.01py311-ont-fast5-apiInterface to HDF5 files in Oxford Nanopore .fast5 format584KiB4.0.2_21py311-pandas-charmLibrary for getting character matrices into and out of pandas34.2KiB0.3.0_3py311-py2bitPython interface for 2bit packed nucleotide files58.0KiB0.3.0_11py311-pyBigWigPython access to bigWig files using libBigWig215KiB0.3.22_12py311-pydeseq2Python implementation of the popular DESeq2 R package540KiB0.5.2_1py311-pyfaidxEfficient pythonic random access to fasta subsequences264KiB0.5.9.5_11py311-pyfastaFast, memory-efficient, pythonic access to fasta sequence files131KiB0.5.2_6py311-pyrodigalPython binding for Prodigal, an ORF finder for genomes and metagenomes5.84MiB3.6.3py311-pysamPython module for reading, manipulating and writing genomic data sets28.1MiB0.23.0_14py311-pyscesPython Simulator for Cellular Systems6.61MiB1.2.2_1py311-python-libsbmlLibSBML Python API50.1MiB5.20.4_11py311-python-nexusGeneric nexus file format reader for python396KiB2.9.0_1py311-pywgsimModified wgsim genomic data simulator328KiB0.5.2_2py311-resdkResolwe SDK to interact with Resolwe server and Resolwe Bioinformatics1.02MiB22.0.0py311-scikit-bioData structures, algorithms, educational resources for bioinformatics18.0MiB0.6.3_1py311-valeriusPython bioinformatics tools30.8KiB0.2_11py311-xenaPythonAPI for Xena Hub to access genetic information shared through the hub125KiB1.0.14_1R-cran-BiobaseBase functions for Bioconductor3.95MiB2.66.01R-cran-BiocGenericsS4 generic functions used in Bioconductor856KiB0.52.01R-cran-BiocManagerConvenient tool to install and update Bioconductor packages1.18MiB1.30.271rainbowEfficient clustering and assembling of short reads, especially for RAD132KiB2.0.41ramplerStandalone module for sampling genomic sequences38.9KiB2.0.0_1readseqRead and reformat biosequences, Java command-line version750KiB2.1.191rna-seqMetaport for RNA-Seq analysis243B0.1.4_1rna-STARSpliced Transcripts Alignment to a Reference1.62MiB2.7.11.a_11ruby33-bioIntegrated environment for Bioinformatics written in Ruby2.60MiB1.5.1rubygem-bioIntegrated environment for Bioinformatics written in Ruby5.43MiB2.0.63rubygem-bio-executablesCollection of miscellaneous utilities for bioinformatics38.5KiB1.0.0rubygem-bio-old-biofetch-emulatorEmulate Bio::Fetch object23.3KiB1.0.01rubygem-bio-shellCommand-line interface on BioRuby114KiB1.0.1salmonTranscript-level quantification of RNA-seq from lightweight alignments9.67MiB1.10.3_1sam2pairwiseShow pairwise alignment for each read in a SAM file43.6KiB1.0.01samtoolsTools for manipulating next-generation sequencing data1.16MiB1.2210scrmCoalescent simulator for biological sequences208KiB1.7.4_1seaviewMultiple DNA/protein sequence alignment editor909KiB5.1,1seqanC++ sequence analysis template library35.1MiB2.4.0seqan1C++ Sequence Analysis Library16.3MiB1.3.1_4seqan3C++ header-only library for biological sequence analysis5.09MiB3.4.0seqkitCross-platform and ultrafast toolkit for FASTA/Q file manipulation19.0MiB2.11.0_41seqtkTool for processing sequences in FASTA/FASTQ format86.8KiB1.52seqwishAlignment to variation graph inducer766KiB0.7.11_2sigviewerViewing application for biosignals935KiB0.6.4.13_2slclustSingle-linkage clustering with Jaccard similarity37.2KiB2010.02.02smithwatermanSmith-waterman-gotoh alignment algorithm355KiBg20160702spoaC++ implementation of the partial order alignment (POA) algorithm342KiB4.1.5sra-toolsNCBI's toolkit for handling data in INSDC Sequence Read Archives168MiB3.3.0_25stacksSoftware pipeline for building loci from short-read sequences7.42MiB2.681stringtieTranscript assembly and quantification for RNA-seq720KiB2.1.11subreadHigh-performance read alignment, quantification and mutation discovery8.14MiB2.1.01tabixppC++ wrapper to tabix indexer64.3KiB1.1.2taxonkitPractical and efficient NCBI taxonomy toolkit10.4MiB0.19.0_13treekinEfficient computation of RNA folding dynamics126KiB0.5.1_7treepuzzleMaximum likelihood phylogeny reconstruction using quartets349KiB5.2trimadapTrim adapter sequences from Illumina data using heuristic rules24.6KiB0.1.41trimmomaticFlexible read trimming tool for Illumina NGS data162KiB0.392tRNAscan-SESearching for tRNA genes in genomic sequence18.2MiB2.0.11ucsc-userappsCommand line tools from the UCSC Genome Browser project100MiB4741ugeneIntegrated bioinformatics toolkit104MiB40.1_1unikmerToolkit for nucleic acid k-mer analysis, set operations on k-mers9.43MiB0.20.0_17vcf-splitSplit a multi-sample VCF into single-sample VCFs19.7KiB0.1.5.10_11vcf2hapGenerate .hap file from VCF for haplohseq11.5KiB0.1.6.7_11vcflibC++ library and CLI tools for parsing and manipulating VCF files11.4MiB1.0.131vcftoolsTools for working with VCF genomics files1.28MiB0.1.171velvetSequence assembler for very short reads958KiB1.2.10_2viennarnaAlignment tools for the structural analysis of RNA136MiB2.7.0_2vsearchVersatile open-source tool for metagenomics560KiB2.30.2vtDiscovers short variants from Next Generation Sequencing data2.14MiB0.57721_31wfa2-libExact gap-affine algorithm using homology to accelerate alignment706KiB2.3.51wiseIntelligent algorithms for DNA searches11.4MiB2.4.1_1