RiboProfilingStarting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3'UTR, and 5'UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.https://bioconductor.org/packages/RiboProfilingriboprofilingbiotools:riboprofiling1.42.0LibraryCommand-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacRGPL-3.0BioConductorhttp://edamontology.org/operation_0286Codon usage analysishttp://edamontology.org/data_1017Sequence rangehttp://edamontology.org/format_2572BAMhttp://bioconductor/packages/release/bioc/src/contrib/RiboProfiling_1.3.2.tar.gzSource codehttps://bioconductor.org/packages/RiboProfilingUser manualAlexandra PopaQuasRThis package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.https://bioconductor.org/packages/Rbowtiequasrbiotools:quasr1.52.0Command-line toolLibraryhttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_3518Microarray experimenthttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0769WorkflowsLinuxWindowsMacRArtistic-2.0BioConductorhttp://edamontology.org/operation_3219Read pre-processinghttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2573SAMhttp://edamontology.org/format_1957rawhttp://edamontology.org/format_1930FASTQhttps://github.com/fmicompbio/RbowtieSource codehttps://bioconductor.org/packages/RbowtieUser manual10.1093/nar/gkq21110.1186/gb-2009-10-3-r25Anita LerchPersonDeveloperFlorian HahnePersonDeveloperMichael StadlerPersonDeveloperMaintainerMUSCLEMUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.https://bioconductor.org/packages/musclemusclebiotools:muscle3.54.0Command-line toolWeb APIhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacUnlicensegalaxyPasteurMUSCLEBioConductorMatureFree of chargeOpen accesshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1936GenBank formathttps://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/oneclick_phylogeny/muscle/3.8.31.1Galaxy servicehttps://www.biocatalogue.org/services/3135Software cataloguehttp://www.drive5.com/muscle/Source codehttps://bioconductor.org/packages/muscleUser manual10.1093/nar/gkh340Algorithm by Robert C. Edgar. R port by Alex T. Kalinka.csawDetection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.https://bioconductor.org/packages/csawcsawbiotools:csaw1.46.0LibraryCommand-line toolhttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifshttp://edamontology.org/topic_3168SequencingLinuxWindowsMacRGPL-3.0BioConductorhttp://edamontology.org/operation_3230Read depth analysishttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_3327BAIhttp://edamontology.org/format_2572BAMhttps://bioconductor.org/packages/release/bioc/src/contrib/csaw_1.46.0.tar.gzSource codehttps://bioconductor.org/packages/csawUser manualAaron LunPersonDeveloperMaintainerGordon SmythPersonDeveloperBiostringsMemory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.https://bioconductor.org/packages/Biostringsbiostringsbiotools:biostrings2.80.2LibraryCommand-line toolhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacRArtistic-2.0BioConductorFree of chargehttp://edamontology.org/operation_1812Loadinghttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_3115Microarray metadatahttp://edamontology.org/format_2061Nucleic acid features (primers) formathttp://edamontology.org/format_1919Sequence record formathttp://edamontology.org/format_2554Alignment format (text)http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2061Nucleic acid features (primers) formathttp://edamontology.org/format_1919Sequence record formathttp://edamontology.org/format_2554Alignment format (text)http://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2061Nucleic acid features (primers) formathttp://edamontology.org/format_1919Sequence record formathttp://edamontology.org/format_2554Alignment format (text)https://bioconductor.org/packages/BiostringsSource codehttps://bioconductor.org/packages/BiostringsUser manual10.18129/B9.bioc.BiostringsAidan LakshmanPersonContributorAlbert VillPersonContributorBeryl KanaliPersonContributorErik WrightPersonContributorFelix ErnstPersonContributorHaleema KhanPersonContributorHervé PagèsPersonDeveloperMaintainerJen WokatyPersonContributorKieran O'NeillPersonContributorMarcel RamosPersonContributorNicolas DelhommePersonContributorPatrick AboyounPersonDeveloperRobert GentlemanPersonDeveloperSaikat DebRoyPersonDeveloperValerie ObenchainPersonContributorVince CareyPersonContributorWolfgang HuberPersonContributorRsubreadAlignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.https://bioconductor.org/packages/Rsubreadrsubreadbiotools:rsubread2.26.0RRID:SCR_016945rridLibraryCommand-line toolhttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_3168SequencingWindowsLinuxMacRGPL-3.0BioConductorhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://edamontology.org/format_2573SAMhttp://bioconductor.org/packages/release/bioc/html/Rsubread.htmlMirrorhttp://bioconductor.org/packages/RsubreadSource codehttps://bioconductor.org/packages/RsubreadUser manual10.1093/nar/gkz114Wei ShiYang Liao and Gordon K Smyth with contributions from Jenny DaigmapRGSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.https://bioconductor.org/packages/gmapRgmaprbiotools:gmapr1.54.0LibraryCommand-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3170RNA-SeqWindowsLinuxMacRArtistic-2.0BioConductorhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttps://bioconductor.org/packages/release/bioc/src/contrib/gmapR_1.54.0.tar.gzSource codehttps://bioconductor.org/packages/gmapRUser manual10.18129/B9.bioc.gmapRCory BarrMichael LawrenceThomas WuGenomicAlignmentsProvides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.https://bioconductor.org/packages/IRangesgenomicalignmentsbiotools:genomicalignments2.46.0LibraryCommand-line toolhttp://edamontology.org/topic_0080Sequence analysisWindowsLinuxMacRArtistic-2.0BioConductorhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_3230Read depth analysishttp://edamontology.org/operation_3563RNA-seq read count analysishttp://edamontology.org/data_1270Feature tablehttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2573SAMhttp://edamontology.org/format_2306GTFhttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://edamontology.org/format_2573SAMhttp://edamontology.org/format_2306GTFhttps://bioconductor.org/packages/IRangesSource codehttps://bioconductor.org/packages/IRangesUser manual10.1371/journal.pcbi.1003118Hervé PagèsPersonDeveloperMaintainerMichael LawrencePersonDeveloperPatrick AboyounPersonDeveloperBBCAnalyzerBBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.https://bioconductor.org/packages/BBCAnalyzerbbcanalyzerbiotools:bbcanalyzer1.42.0LibraryCommand-line toolhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0080Sequence analysisWindowsLinuxMacRLGPL-3.0BioConductorhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttps://bioconductor.org/packages/release/bioc/src/contrib/BBCAnalyzer_1.42.0.tar.gzSource codehttps://bioconductor.org/packages/BBCAnalyzerUser manual10.18129/B9.bioc.BBCAnalyzerSarah SandmannBaseSpaceRA rich R interface to Illumina's BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.https://bioconductor.org/packages/BaseSpaceRbasespacerbiotools:basespacer1.56.0LibraryCommand-line toolhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3372Software engineeringWindowsLinuxMacRApache-2.0BioConductorhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1930FASTQhttps://bioconductor.org/packages/release/bioc/src/contrib/BaseSpaceR_1.56.0.tar.gzSource codehttps://bioconductor.org/packages/BaseSpaceRUser manual10.18129/B9.bioc.BaseSpaceRAdrian AlexabamsignalsThis package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.https://bioconductor.org/packages/bamsignalsbamsignalsbiotools:bamsignals1.44.1LibraryCommand-line toolhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0080Sequence analysisMacWindowsLinuxRGPL-2.0BioConductorhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttps://github.com/lamortenera/bamsignalsSource codehttps://bioconductor.org/packages/bamsignalsUser manual10.18129/B9.bioc.bamsignalsAlessandro MammanaPersonDeveloperMaintainerJohannes HelmuthPersonDevelopersystemPipeRsystemPipeR is a workflow management environment for reproducible data analysis that integrates R with command-line software. It enables researchers to design, execute, and report complex workflows on local machines and HPC systems. The framework combines R-based analysis with external tools through a Common Workflow Language (CWL) interface, manages workflow dependencies and restart capabilities, and automatically generates reproducible scientific analysis reports. The companion package systemPipeRdata provides ready-to-use workflow templates that simplify workflow setup and customization. Alternatively, workflow templates can be loaded from dedicated GitHub repositories.https://bioconductor.org/packages/systemPipeRsystempiperbiotools:systempiper2.18.0LibraryCommand-line toolhttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_3170RNA-SeqMacLinuxWindowsRArtistic-2.0BioConductorhttp://edamontology.org/operation_3680RNA-Seq analysishttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_3020BCFhttp://edamontology.org/format_2572BAMhttps://github.com/tgirke/systemPipeRMirrorhttps://github.com/tgirke/systemPipeRSource codehttps://bioconductor.org/packages/systemPipeRUser manual10.1186/s12859-016-1241-010.1186/s12859-016-1241-0Thomas GirkeRsamtoolsThis package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.https://bioconductor.org/packages/Rsamtoolsrsamtoolsbiotools:rsamtools2.28.0Command-line toolLibraryhttp://edamontology.org/topic_3170RNA-SeqWindowsLinuxMacRArtistic-2.0SAMtools utilityBioConductorhttp://edamontology.org/operation_3563RNA-seq read count analysishttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_3219Read pre-processinghttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://edamontology.org/format_3616tabixhttp://edamontology.org/format_3020BCFhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_2573SAMhttp://bioconductor.org/packages/release/bioc/html/Rsamtools.htmlMirrorhttps://bioconductor.org/packages/RsamtoolsSource codehttps://bioconductor.org/packages/RsamtoolsUser manual10.18129/B9.bioc.RsamtoolsBioconductor Package MaintainerPersonMaintainerBusayo SamuelPersonContributorHervé PagèsPersonDeveloperMartin MorganPersonDeveloperNathaniel HaydenPersonDeveloperValerie ObenchainPersonDeveloperMUSCLE (EBI)MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.https://bioconductor.org/packages/musclemuscle_ebibiotools:muscle_ebi3.54.0RRID:SCR_011812rridWeb applicationWeb servicehttp://edamontology.org/topic_0080Sequence analysisWindowsLinuxMacUnlicenseEBI ToolsJob Dispatcher ToolsBioConductorMUSCLEhttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttps://www.ebi.ac.uk/about/contact/support/job-dispatcher-servicesHelpdeskhttp://www.drive5.com/muscle/Source codehttps://bioconductor.org/packages/muscleUser manualmuscleuses10.1093/nar/gkh340Algorithm by Robert C. Edgar. R port by Alex T. Kalinka.msaThe 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.https://bioconductor.org/packages/msamsabiotools:msa1.44.1LibraryCommand-line toolhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_3168SequencingMacLinuxWindowsJavaScriptGPL-2.0-or-laterRostlab toolsBioconductorBioJSBioConductorMatureFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1984FASTA-alnVisualizes multiple sequence alignment, calculates conservation, shows sequence logo, applies multiple color schemes A multiple sequence alignment (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment Images are exported in PNG Export sequences in FASTA format Export features in GFF
NOTE: Actually, all these output types of data should instead be under separate "constant" operations, while the visualisation should be an unary operation, perhaps without an output.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1948nbrf/pirhttp://github.com/wilzbach/msaHelpdeskhttp://www.bioinf.jku.at/software/msa/Mirrorhttps://github.com/wilzbach/msaRepositoryhttp://biojs.io/Software cataloguehttps://github.com/UBod/msaSource codehttps://bioconductor.org/packages/msaUser manual10.1093/bioinformatics/btv494Christoph KainrathPersonDeveloperEnrico BonatestaPersonDeveloperUlrich BodenhoferPersonDeveloperMaintainerBSgenomeInfrastructure shared by all the Biostrings-based genome data packages.https://bioconductor.org/packages/BSgenomebsgenomebiotools:bsgenome1.80.0LibraryCommand-line toolhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0080Sequence analysisWindowsLinuxMacRArtistic-2.0BioConductorhttp://edamontology.org/operation_0368Sequence maskinghttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_1812Loadinghttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_1919Sequence record formathttps://bioconductor.org/packages/BSgenomeSource codehttps://bioconductor.org/packages/BSgenomeUser manual10.18129/B9.bioc.BSgenomeHervé PagèsPersonDeveloperMaintainerD-GENIESD-GENIES – for Dot plot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualization.https://dgenies.toulouse.inrae.fr/d-geniesbiotools:d-geniesCommand-line toolWeb applicationhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0080Sequence analysisMacLinuxShellPythonGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3182Genome alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/operation_0490Dot plot plottinghttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttps://github.com/genotoul-bioinfo/dgeniesRepositoryhttps://dgenies.readthedocs.io/en/latest/index.htmlGeneral10.7717/peerj.495829888139PMC5991294PrimaryFloréal CabanettesPersonDeveloperChristophe Kloppchristophe.klopp@inrae.frhttps://orcid.org/0000-0001-7126-5477PersonPrimary contactPhilippe Bordronhttps://orcid.org/0000-0003-1975-0920PersonPrimary contactDeveloperVincent DominguezDeveloperGenoToul bioinformatics facilityhttp://bioinfo.genotoul.fr/DivisionProviderab1lensBrowser-based viewer for Sanger sequencing chromatograms in AB1/ABIF and SCF format, and for the .srd raw files of the Nanofor-05 capillary sequencer, converted to ABIF as they open. Shows raw and analysed traces, base calls (called or edited), per-base quality and the full ABIF directory, and puts two reads side by side with their tag tables aligned. A read aligns against a pasted or loaded reference, which reports identity, mismatches, indels and the ends that did not align, and flips the strand when the read is on the other one. End trimming (modified Mott or sliding window) has draggable handles, motif search is IUPAC-aware and finds primers, and QC metrics copy out as CSV. Drag on a trace to select a base range, then copy it as FASTA, zoom to it or export just that region. Exports the read as FASTA, FASTQ, .qual or ABIF and the chromatogram as a high-resolution PNG. Open files are kept as local sessions. Runs entirely in the browser — files are never uploaded.https://fishka.bio/ab1lensab1lensbiotools:ab1lensDesktop applicationWeb applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationWindowsLinuxMacTypeScriptFreewarefishka.bioMatureFree of chargeOpen accesshttp://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/operation_0363Reverse complementhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3000AB1http://edamontology.org/format_1632SCFhttp://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3000AB1http://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1929FASTAhttps://fishka.bioSoftware cataloguefishka.bio — the tool collection ab1lens belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no serverhttps://fishka.bio/ab1lens/showcaseTraining materialShowcase gallery — an annotated screenshot per task, from quality control to aligning a read against a reference10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including ab1lens.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainerreadhitBrowser-based viewer that maps sequencing reads onto one short reference — an amplicon, gene or plasmid. Reads open as Sanger AB1/ABIF, SCF, FASTA, FASTQ or a SAM somebody else already mapped (gzipped files are unpacked in place); the reference as FASTA, GenBank or a read. Both read orientations are tried automatically. The pileup reports per-position depth, where reads disagree with the target, and the consensus — phred-weighted for capillary reads, which keep their chromatogram under the letters. An optional protein lane translates target and consensus side by side. Reads are placed by minimap2 compiled to WebAssembly, or by the built-in aligner. One read or the whole alignment saves as FASTA. Runs entirely in the browser — files are never uploaded.https://fishka.bio/readhitreadhitbiotools:readhitWeb applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0199Genetic variationWindowsMacLinuxTypeScriptFreewarefishka.bioEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_2573SAMhttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3000AB1http://edamontology.org/format_1632SCFhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAMhttps://fishka.bioSoftware cataloguefishka.bio — the tool collection readhit belongs tohttps://fishka.bio/readhit/showcaseTraining materialShowcase gallery — an annotated screenshot per task, from a handful of Sanger reads to an NGS pileup opened from a SAMFishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainerNEXCISIONExact, validated excision of coordinate-defined genomic regions from transposed NEXUS matrices.https://github.com/RhysWhite/nexcisionnexcisionbiotools:nexcision0.1.1doi:10.5281/zenodo.21936049doi0.1.1Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3293PhylogeneticsLinuxMacWindowsPythonMITEmergingFree of chargehttp://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1949nexus-seqhttp://edamontology.org/data_1017Sequence rangeRemove coordinate-labelled NEXUS matrix rows overlapping user-defined 1-based inclusive genomic regions.nexcise NEXUS REGIONS [options]https://github.com/RhysWhite/nexcisionRepositorySource code and development repository.https://github.com/RhysWhite/nexcision/issuesIssue trackerBug reports and feature requests.https://github.com/RhysWhite/nexcision-benchmarkingRepositoryIndependent validation, adversarial testing, and scalability benchmarking materials.https://github.com/RhysWhite/nexcision/releases/tag/v0.1.1Source codeTagged NEXCISION v0.1.1 source release.0.1.1https://pypi.org/project/nexcision/0.1.1/Software packagePython package for installation with pip.0.1.1https://anaconda.org/bioconda/nexcisionSoftware packageBioconda package for Conda-based environments.0.1.1https://nexcision.readthedocs.io/GeneralHosted NEXCISION documentation.https://nexcision.readthedocs.io/en/latest/installation/Installation instructionsInstallation via PyPI, Bioconda, or tagged GitHub releases.https://nexcision.readthedocs.io/en/latest/workflow-integration/User manualWorkflow integration, provenance reporting, validation policies, and Snakemake examples.10.64898/2026.07.26.740842PreprintPrimary NEXCISION methods and validation preprint.Rhys Whiterhys.white@phfscience.nzhttps://www.phfscience.nz/staff-profiles/rhys-white/https://orcid.org/0000-0001-6620-758XPersonPrimary contactDeveloperMaintainerProteinsPlusThe ProteinsPlus web server aims to support life scientists in working with protein structures. Protein structures are the key to understanding protein function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. ProteinsPlus focuses on protein-ligand interactions. The server provides support for the initial steps of dealing with protein structures, namely structure search, quality assessment, and preprocessing. JAMDA enables users to perform an on-the-fly molecular docking of up to five molecules. The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced options, such as protein pocket detection (DoGSite), prediction of water molecule positions (WarPP), protein structure ensemble generation (SIENA), prediction of metal coordination (METALizer), the analysis of solvent channels in protein crystals (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.https://proteins.plusproteinsplusbiotools:proteinsplusWeb serviceWeb APIhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMacOtherde.NBIde.NBI-biodataMatureFree of chargeTools3D-BioInfoGermanyhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprediction of protonation states and tautomers and placement of hydrogen atomshttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_1844Protein geometry validationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFquality profiling for protein-ligand complexeshttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0384Accessible surface calculationhttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFcalculating bottleneck radii for crystal solvent channelshttp://edamontology.org/operation_0321Protein structure validationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFatom-level assessment of the electron density fit for structures solved by X-ray crystallographyhttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBprotein-protein interface classification (permanent, transient, crystal artifact)http://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1197InChIhttp://edamontology.org/format_1196SMILEShttp://edamontology.org/format_3816Mol2http://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFprotein-ligand docking for small moleculeshttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detectionhttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFsmall molecule binding site detection and druggability assessmenthttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawing and editinghttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFmetal complex geometry predictionhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_1839Salt bridge calculationhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_1834Protein-metal contact calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDF2D interaction diagram drawinghttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFstructural single-residue substitution search and analysishttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFPDB mining and protein binding site ensemble generationhttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFtextual, numerical, and chemical 3D searches in the PDBhttp://edamontology.org/operation_0394Hydrogen bond calculationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFwater molecule placementhttps://proteins.plusServicehttps://proteins.plus/help/indexGeneraldogsitescorerincludesdogsite3includesediaincludessienaincludesmetalizerincludesstructureprofilerincludesjamdaincludesgeomineincludesmicrominerincludesposeeditincludesposeviewincludesprotossincludeslifesoaksincludesppiincludes10.1093/nar/gkx33328472372PMC5570178Primary10.1093/nar/gkaa23532297936PMC7319454Usage10.1093/nar/gkac30535489057PMC9252762Usage10.1093/nar/gkaf37740326518PMC12230695UsageProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProviderSIENASIENA is a software pipeline enabling the fully automated construction of protein structure ensembles from the PDB. Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and superimposed. SIENA also handles complicated cases, such as comparing binding sites at protein domain interfaces or within multimeric proteins.https://www.zbh.uni-hamburg.de/en/forschung/amd/software/siena.htmlsienabiotools:sienaCommand-line toolWeb APIWeb servicehttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0128Protein interactionsMacWindowsLinuxOtherde.NBI-biodatade.NBIMatureFree of charge (with restrictions)Tools3D-BioInfoGermanyhttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_0509Local structure alignmenthttp://edamontology.org/operation_0244Simulation analysishttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_0339Structure database searchhttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_3814SDFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_3814SDFPDB mining and protein binding site ensemble generationhttps://proteins.plusServiceA web service to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://proteins.plus/help/siena_restServiceA web API to run SIENA calculations for protein structures stored in the Protein Data Bank and AlphaFold Protein Structure Database or uploaded structures.https://uhh.de/naomiSoftware catalogueA link to download the standalone tool from the NAOMI ChemBio Suite.https://uhh.de/naomiBinariesPlease register to download the tool.https://proteins.plus/help/indexGeneralproteinsplusincludedIn10.1021/acs.jcim.5b0058826759067MethodPrimary10.1021/acs.jcim.5b0021026098831MethodProteinsPlus Supportpplus.zbh@uni-hamburg.dePrimary contactPrimary Contact for Web Service IssuesNAOMI ChemBio Suite Supportsoftware.zbh@uni-hamburg.dePrimary contactPrimary Contact for Standalone Tool IssuesUniversity of Hamburg, ZBH - Center for Bioinformatics00g30e956InstituteProvidernalloNallo is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects a wide range of genetic variants, performs genome assembly,
and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional
consequences.https://github.com/genomic-medicine-sweden/nallonallobiotools:nallo0.12.0http://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3673Whole genome sequencinghttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_3295EpigeneticsGroovyJavaMITFree of chargehttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2545FASTQ-like formathttps://github.com/genomic-medicine-sweden/nalloRepositoryhttps://genomic-medicine-sweden.github.io/nallo/latest/User manual10.1093/BIOINFORMATICS/BTAG08641712762PMC12988770Lars Feuklars.feuk@igp.uu.sehttps://orcid.org/0000-0003-2355-2919PersonSPALNGenome mapping and spliced alignment of cDNA or amino acid sequenceshttps://github.com/ogotoh/spalnspalnbiotools:spalnver.3.0.8bCommand-line toolhttp://edamontology.org/topic_0102MappingCPerlC++GPL-2.0Maturehttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_1234Sequence set (nucleic acid)https://github.com/ogotoh/spalnRepositoryhttps://github.com/ogotoh/spalnGeneral10.1093/nar/gkag35742134803PMC1317563310.1093/bioinformatics/btn4601872804310.1093/nar/gks70822848105PMC348821110.1093/bioinformatics/16.3.1901086901210.1093/bioinformatics/btae51739152995PMC1136180910.1007/978-1-0716-1036-7_53328988710.1093/bioinformatics/btl06716500940Osamu Gotohgotoh.osamu.67a@st.kyoto-u.ac.jphttps://orcid.org/0009-0002-6750-1945PersonVerityMapVerityMap is a tool for mapping long reads to assemblies of extra-long tandem repeats, producing SAM files and identifying potential heterozygous sites and assembly errors through analysis of rare k-mers. It supports PacBio HiFi and ONT reads and generates interactive HTML plots for variant analysis.https://github.com/ablab/VerityMapVerityMapbiotools:VerityMaphttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0622GenomicsCCUDAPythonC++GPL-3.0Maturehttp://edamontology.org/operation_0523Mapping assemblyhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/ablab/tandemQUAST/issuesIssue tracker10.1093/bioinformatics/btaa44032657355PMC7355294SNP-sitesFinds SNP sites from a multi-FASTA alignment file.https://sanger-pathogens.github.io/snp-sites/snp-sitesbiotools:snp-sites2.5.1Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_2885DNA polymorphismLinuxCGPL-3.0Open accesshttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_3820Relaxed PHYLIP Sequentialhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3016VCFsnp-sites my_alignment.aln
snp-sites my_gzipped_alignment.aln.gzhttps://github.com/sanger-pathogens/snp-sitesRepositoryhttps://sanger-pathogens.github.io/snp-sites/General10.1099/mgen.0.00005628348851PMC5320690Primarysam2intervalA Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2intervalsam2intervalbiotools:sam2intervalScripthttp://edamontology.org/topic_0622GenomicsMacWindowsLinuxPythonMITEmergingFree of chargeOpen accessGalaxyhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAMhttps://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2intervalRepositoryRepeatAfterMeRepeatAfterMe is a package for the extension of repetitive DNA cores. The tool automatically extends a multiple sequence alignment that may represent only a fragment of a longer repetitive sequence family.https://github.com/Dfam-consortium/RepeatAfterMerepeataftermebiotools:repeataftermev0.0.7Command-line toolhttp://edamontology.org/topic_0622GenomicsMacLinuxCCC0-1.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_30092bithttp://edamontology.org/data_1017Sequence rangehttp://edamontology.org/format_3585bed6./RAMExtend -ranges test/extension-test2.tsv -twobit test/extension-test2.2bitRobert HubleyPersonDeveloperslow5-doradoFork of dorado (high-performance, easy-to-use, open source analysis engine for Oxford Nanopore reads) that support S/BLOW5https://github.com/hiruna72/slow5-doradoslow5-doradobiotools:slow5-dorado1.1.1Command-line toolhttp://edamontology.org/topic_4056Long-read sequencinghttp://edamontology.org/topic_0080Sequence analysisLinuxC++Otherhttp://edamontology.org/operation_3185Base-callinghttp://edamontology.org/data_0924Sequence tracebwa-methbwa-meth is a tool for alignment of Bisulfite sequencing reads.https://github.com/brentp/bwa-methbwa-methbiotools:bwa-meth0.2.9Command-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0622GenomicsLinuxPythonMITMatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQ10.48550/arXiv.1401.1129PreprintPLASTPLAST is a heuristical method to search for highest scoring local alignments between a DNA sequence query and a graphical pangenome. It takes as input a plain DNA sequence and a pangenome which may either be a set of (multiple) FASTA or FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard output format. Alignments are calculated based on a "seed-and-extend approach" while traversing the sequence graph. Biologically meaningful alignments are filtered by using an alignment statistic explicitly developed for sequence-to-graph alignments involving graphical pangenomes.https://github.com/tischulz1/plastpangenome-blastbiotools:pangenome-blast0.0.1-0.2.0Command-line toolhttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0080Sequence analysisLinuxMacWindowsC++GPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1211unambiguous pure nucleotidehttp://edamontology.org/data_1234Sequence set (nucleic acid)http://edamontology.org/format_3975GFA 1http://edamontology.org/format_2333Binary formatIn order to search for alignments within the pangenome graph,
A pangenome graph used to search for alignments consists of (1) a file in GFA format containing all sequences of the graph, (2) a binary file produced by the tool itself or the software "Bifrost" and (3) a program-specific index data structure in binary format.PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLinehttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1930FASTQIf a pangenome graph already exists and only an index has to be built, FASTA/FASTQ files are not needed.PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fastahttps://gitlab.ub.uni-bielefeld.de/gi/plastRepositoryhttps://github.com/tischulz1/plastMirrorhttps://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.mdGeneral10.1093/bioinformatics/btab07733532821PMC8388040PrimaryMethodBenchmarking studyBielefeld Universityhttps://www.uni-bielefeld.de/InstituteProviderGenome Informaticshttps://gi.cebitec.uni-bielefeld.de/InstituteProviderTizian Schulzplast-service@cebitec.uni-bielefeld.dehttps://orcid.org/0000-0003-0744-7078PersonDeveloperBioMaS (Bioinformatic analysis of Metagenomic amplicons)BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills.http://itsonewb.cloud.ba.infn.it/galaxy/tool_runner?tool_id=biomas2_wrapperbiomas_bioinformatic_analysis_of_metagenomic_ampliconsbiotools:biomas_bioinformatic_analysis_of_metagenomic_amplicons1.0Web applicationhttp://edamontology.org/topic_3391OmicsLinuxMacWindowsBashPythonNot licensedEmergingFree of charge (with restrictions)Open access (with restrictions)ToolsMarine MetagenomicsItalyhttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_2573SAMhttp://edamontology.org/operation_0232Sequence merginghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_0496Global alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQ10.1186/s12859-015-0595-z26130132PMC4486701MethodBruno Fossob.fosso@ibiom.cnr.ithttps://orcid.org/0000-0003-2324-086XPersonDeveloperResearcher at CNR-IBIOMGraziano Pesolegraziano.pesole@uniba.ithttps://orcid.org/0000-0003-3663-0859PersonPrimary contactFull Professor of Molecular Biology at University of BariMonica Santamariam.santamaria@ibiom.cnr.ithttps://orcid.org/0000-0003-1488-6052PersonContributorResearcher at CNR-IBIOMJalviewJalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.https://www.jalview.org/Jalviewbiotools:Jalview2.11.5.1Desktop applicationCommand-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsGPL-3.0ELIXIR-UKMatureFree of chargeOpen accessToolsInteroperabilityUKhttp://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/operation_0324Phylogenetic tree analysishttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1984FASTA-alnhttp://edamontology.org/format_3015Pileuphttp://edamontology.org/format_1938GFF2-seqhttp://edamontology.org/format_3313BLChttp://edamontology.org/format_3311RNAMLhttp://edamontology.org/format_1915Formathttp://edamontology.org/format_3774BioJSON (Jalview)http://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1939GFF3-seqhttp://edamontology.org/format_1947GCG MSFhttp://edamontology.org/data_0886Structure alignmenthttp://edamontology.org/format_1476PDBOther Input formats:
AMSA (.amsa);
JnetFile (.concise, .jnet);
PFAM (.pfam);
Substitution matrix (.matrix);
Jalview Project File (.jvp);
Jalview Feature File (.features, .jvfeatures);
Jalview Annotations File (.annotations, .jvannotations);
Predicted Aligned Error (PAE) Matrix File (.json)
...
Other Output formats:
PFAM (.pfam);
BioJS (.biojs) (interactive HTML/Javascript);
Jalview Project File (.jvp);https://discourse.jalview.org/Discussion forumhttps://issues.jalview.org/Issue trackerhttps://www.jalview.org/development/jalview_develop/OtherLatest development versionhttps://gitlab.jalview.org/jalview/jalview.gitRepositoryhttps://twitter.com/JalviewSocial mediaTwitter feedhttps://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfwSocial mediaYouTube training videoshttps://www.linkedin.com/company/104771886/Social mediahttps://www.jalview.org/downloadDownloads pagehttps://www.jalview.org/download/source/Source codehttps://www.jalview.org/download/?os=allBinariesBinaries for all platformshttps://www.jalview.org/favicon.svgIconhttps://www.jalview.org/download/other/jar/BinariesExecutable JAR filehttps://www.jalview.org/about/citationCitation instructionshttps://www.jalview.org/training/Training materialHands-on exercises, Training courses and Training videoshttps://www.jalview.org/help/faqFAQhttps://www.jalview.org/help/documentation/User manualjabawsuseschimerauseschimeraxusespymolusesbiocondaincludedIn3d-beaconsusesuniprotusespfamusesensemblusespdbusesrfamuses3d-beaconsuses10.1093/bioinformatics/btp03319151095PMC2672624Jim Procterhttp://www.lifesci.dundee.ac.uk/people/jim-procterhttps://orcid.org/0000-0002-7865-7382PersonPrimary contactGeoff Bartonhttps://www.lifesci.dundee.ac.uk/people/geoff-bartonhttps://orcid.org/0000-0002-9014-5355SILVA rRNA databaseSILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).https://www.arb-silva.desilvabiotools:silvaRRID:SCR_006423rridWeb applicationDatabase portalhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0632Probes and primersCC-BY-4.0de.NBIde.NBI-biodataDSMZ Digital DiversityMatureFree of chargeOpen accessDataGermanyhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1097Sequence accession (nucleic acid)http://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1868Taxonhttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1046Strain namehttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1088Article IDhttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_2909Organism namehttp://edamontology.org/format_1964plain text format (unformatted)The search and retrieval functions of the SILVA website can be used to build custom subsets of sequences. In addition to simple searches e.g. for accession numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs, complex queries over several database fields using constraints such as sequence length or quality values are possible. The results can be sorted according to accession numbers, organism names, sequence length, sequence and alignment quality and Pintail values. The search results show accession number, organism name, sequence length, sequence quality values, taxonomic classifications, and links to view the full sequence record on SILVA and on ENA. Sequences found via search and added to download cart can be downloaded as FASTA and ARB files.http://edamontology.org/operation_2419Primer and probe designhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1207nucleotidehttp://edamontology.org/data_1240PCR primershttp://edamontology.org/format_1207nucleotideThe SILVA Probe Match and Evaluation Tool detects and displays all occurrences of a given probe or primer sequence in the SILVA datasets.
TestPrime allows you to evaluate the performance of primer pairs by running an in silico PCR on the SILVA databases. From the results of the PCR, TestPrime computes coverages for each taxonomic group in all of the taxonomies offered by SILVA.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0496Global alignmenthttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/operation_0547Phylogenetic inference (maximum likelihood and Bayesian methods)http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1984FASTA-alnThe Alignment, Classification and Tree Service (ACT) of SILVA allows to align and optionally classify sequences using the SILVA Incremental Aligner (SINA). From aligned sequences, (optionally) phylogenetic trees can be inferred using FastTree or RAxML.https://www.arb-silva.de/browser/ServiceSILVA Taxonomy Browserhttps://www.arb-silva.de/search/ServiceSILVA metadata searchhttps://www.arb-silva.de/aligner/ServiceACT: Alignment, Classification and Tree Servicehttps://www.arb-silva.de/search/testprobe/ServiceSILVA Probe Match and Evaluation Toolhttps://www.arb-silva.de/search/testprime/ServiceSILVA Primer Evaluation Toolhttps://treeviewer.arb-silva.de/ServiceWeb-based viewer for the SILVA guide treeshttps://www.arb-silva.de/download/archive/Downloads pageSILVA dataset archivehttps://www.arb-silva.de/silva-license-information/Terms of usehttps://www.arb-silva.de/contact/Citation instructionshttps://www.arb-silva.de/documentation/Generalhttps://www.arb-silva.de/documentation/faqs/FAQsilvangsusedByd3hubincludedIn10.1093/nar/gks121923193283PMC3531112Primary10.1093/nar/gkt120924293649PMC3965112Other10.1093/nar/gkm86417947321PMC2175337Other10.1093/bioinformatics/bts25222556368PMC3389763Other10.1016/j.jbiotec.2017.06.119828648396Review10.1186/s12859-017-1841-3OtherLeibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultureshub@dsmz.dehttps://www.dsmz.degrid.420081.f02tyer376InstituteProviderSILVA Teamcontact@arb-silva.dehttps://www.arb-silva.de/contact/team/grid.507782.f027z9pz32DivisionPrimary contactZoonomiaThe Zoonomia Project provides access to genomic data including assemblies, annotations and alignments for 240 mammalian species.https://zoonomiaproject.org/zoonomiaprojectbiotools:zoonomiaprojectDatabase portalhttp://edamontology.org/topic_3050BiodiversityMatureFree of chargeOpen accesshttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_2909Organism namehttp://edamontology.org/data_1045Species nameMuGVREThe MuG Virtual Research Environment is an analysis platform for 3D/4D genomics analyses. It integrates genomics tools for chromatin dynamics data.https://www.multiscalegenomics.eu/mugvrebiotools:mugvre1.0Web applicationWorkbenchhttp://edamontology.org/topic_3176DNA packaginghttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_2275Molecular modellingPHPPythonApache-2.0RIS3CAT VEISFree of chargeOpen accesshttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3210Genome indexhttp://edamontology.org/operation_0475Nucleic acid structure predictionhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_0279Nucleic acid folding analysishttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_2305GFFhttp://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/operation_3900DNA-binding protein predictionhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_3222Peak callinghttp://edamontology.org/operation_1781Gene regulatory network analysishttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_2572BAMhttp://edamontology.org/operation_3927Network analysishttp://edamontology.org/operation_0279Nucleic acid folding analysishttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_2481Nucleic acid structure analysishttp://edamontology.org/data_0883Structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_0432Nucleosome position predictionhttp://edamontology.org/operation_3454Phasinghttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_2572BAMhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/data_3869Simulationhttp://edamontology.org/data_0883Structurehttp://vre.multiscalegenomics.euServicehttps://github.com/Multiscale-Genomics/VRERepositoryhttps://www.multiscalegenomics.eu/MuGVRE/terms-of-use/Terms of usehttp://vre.multiscalegenomics.eu/help/starting.phpQuick start guidehttps://www.multiscalegenomics.eu/MuGVRE/training/Training materialnucleosome_dynamicsincludestadbitincludesjbrowseincludesnglincludes10.1101/602474Primary1.0Laia Codólaia.codo@bsc.eshttps://orcid.org/0000-0002-6797-8746PersonPrimary contactJosep Lluís Gelpíhttp://orcid.org/0000-0002-0566-7723PersonContributorMultiscale Complex Genomics Communityvre@multiscalegenomics.euhttps://www.multiscalegenomics.eu/ConsortiumDeveloperBioSurfDBBioSurfDB is a online database for biodegradation and biosurfactants.https://www.biosurfdb.orgbiosurfdbbiotools:biosurfdbDatabase portalhttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0821EnzymesMatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/operation_0349Sequence database search (by property)10.1093/database/bav033PrimaryJorge S. Oliveirajorge.oliveira@tecnico.ulisboa.pthttps://web.tecnico.ulisboa.pt/jorge.oliveira/https://orcid.org/0000-0001-6425-2176PersonPrimary contactAna Teresa Freitasana.freitas@tecnico.ulisboa.pthttp://orcid.org/0000-0003-4638-2879PersonPrimary contactAna Tereza Ribeiro de Vasconcelosatrv@lncc.brhttp://orcid.org/0000-0002-4632-2086PersonPrimary contactLucymara Fassarella Agnez-Limalucymara.agnez@ufrn.brhttp://orcid.org/0000-0003-0642-3162PersonPrimary contactGil Poiares-Oliveiragpo@biodata.pthttps://web.tecnico.ulisboa.pt/gil.oliveirahttps://orcid.org/0000-0003-4638-2879PersonMaintainersamclipFilter SAM file for soft and hard clipped alignmentshttps://github.com/tseemann/samclipsamclipbiotools:samclip0.4.0Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0102MappingLinuxMacPerlhttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttps://github.com/tseemann/samclipRepositoryhttps://anaconda.org/bioconda/samclipSoftware package0.4.0https://github.com/tseemann/samclipGeneralTREND Protein Evolution FunctionTREND is a platform that allows researchers to explore protein function and evolution identifying protein features, gene neighborhoods and operons, clustering neighboring genes, and integrating all these data into phylogenomic context and cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides ample opportunities for adjusting each step of the analysis.http://trend.evobionet.com/trend_protein_evolution_functionbiotools:trend_protein_evolution_functionWeb servicehttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_0194Phylogenomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0323Phylogenetic inferencehttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_2995Sequence classificationhttp://edamontology.org/operation_0246Protein domain recognitionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_1384Protein sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_1900NCBI locus taghttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2385RefSeq accession (protein)http://trend.evobionet.com/helpUser manual10.1093/nar/gkaa24332282909PMC7319448Primary10.1093/nar/gkac03435100406PMC8860576OtherCan be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937Vadim Gumerovgumerov.1@osu.eduhttps://orcid.org/0000-0003-1670-7679CrispiA CRISPR Interactive database.http://crispi.genouest.org/crispibiotools:crispiDatabase portalhttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAA CRISPR Interactive databasehttp://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/CRISPR/help/crispri.pdfGeneral10.1093/bioinformatics/btp58619846435PMC2788928PrimaryGenOuestInstituteProviderGenOuest platformsupport@genouest.orghttp://www.genouest.orgPersonPrimary contactPlastParallel Local Alignment Search Tool for Database Comparison.http://www.irisa.fr/symbiose/projects/plast/plastbiotools:plast1.0Command-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCECILL-2.0MatureFree of chargehttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTASequence alignmenthttps://plast.inria.fr/General10.1186/1471-2105-10-32919821978PMC2770072PrimaryGenOuestInstituteProviderDominique Lavenierlavenier@irisa.frPersonPrimary contactCyanoLyaseManually curated sequence and amino acid motif database gathering all the different phycobilin lyases and related protein sequences available in public databases.http://cyanolyase.genouest.org/cyanolyasebiotools:cyanolyaseDatabase portalhttp://edamontology.org/topic_0623Gene and protein familiesLinuxWindowsMacMatureFree of chargehttp://edamontology.org/operation_0253Sequence feature detectionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAMotif occurence detection in protein sequenceshttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAProtein sequence alignment against known family membershttp://cyanolyase.genouest.org/helpGeneral10.1093/nar/gks109123175607PMC3531064PrimaryGenOuestInstituteProviderGenOuestsupport@genouest.orghttp://www.genouest.orgPersonPrimary contactSliderA suite of java classes which provides alignment of Illumina Sequence analyser reads. For alignment it uses base probabilities instead of sequences. It also enambles SNP prediction.http://www.bcgsc.ca/platform/bioinfo/software/slidersliderbiotools:sliderSuitehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_2533DNA mutationhttp://edamontology.org/topic_2269Statistics and probabilityLinuxWindowsMacJavaAFL-3.0http://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2959Nucleic acid probability profilehttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/data_2093Data referencehttp://edamontology.org/format_3033Matrix format10.1093/bioinformatics/btn56518974170PMC2638935Slider supportnmalhis@bcgsc.caPersonPrimary contactwebPRANKMultiple sequence alignment tool.http://www.ebi.ac.uk/goldman-srv/webprank/webprankbiotools:webprank1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacGoldman ToolsEBI Toolshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/goldman-srv/webprank/General10.1186/1471-2105-11-57921110866PMC3009689PrimaryGoldman groupPersonDeveloperAri LoytynojaPersonDeveloperNick GoldmanContributorEMBL-EBIInstituteProviderari@ebi.ac.ukPersonPrimary contactAri Loytynojaari.loytynoja@helsinki.fiPersonPrimary contactSASAnnotation of protein sequence with structural info from similar proteins in the PDB.http://www.ebi.ac.uk/thornton-srv/databases/sassasbiotools:sas1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacThornton ToolsEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_2976Protein sequenceThe ouput is an alignment of the query sequence vs a sequence from PDB, annotated by structural datahttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/thornton-srv/databases/sasGeneral10.1093/protein/11.10.8559862203PrimaryRoman LaskowskiPersonDeveloperThornton GroupPersonDeveloperDuncan MilburnContributorEMBL-EBIInstituteProviderroman@ebi.ac.ukPersonPrimary contactRoman Laskowskiroman@ebi.ac.ukPersonPrimary contactleBIBIpqpThe BioInformatics Prokaryotes Quick Phylogeny is designed to reconstruct the phylogeny of an Archaea or a Bacteria from its nucleic acid sequence. It is also giving the useful informations if species identification is needed.https://umr5558-bibiserv.univ-lyon1.fr/lebibi/lebibi.cgilebibipqpbiotools:lebibipqp6.0Web applicationhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0621Model organismsLinuxWindowsMacFree of chargehttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0258Sequence alignment analysishttp://edamontology.org/operation_0338Sequence database searchhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1056Database namehttps://umr5558-bibiserv.univ-lyon1.fr/BIBIDOCNEW/index.html#lebibi-qbpp-documentationGeneral10.1186/s12859-015-0692-z26264559PMC4531848IFB ELIXIR-FRInstituteProviderJean-Pierre Flandroisjean-pierre.flandrois@univ-lyon1.frPersonPrimary contactSeaViewMultiplatform graphical user interface designed to facilitate alignment and phylogenic tree building from molecular sequences.http://doua.prabi.fr/software/seaviewseaviewbiotools:seaview4Command-line toolDesktop applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0084PhylogenyLinuxWindowsMachttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0326Phylogenetic tree editinghttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0540Phylogenetic tree generation (from molecular sequences)http://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/data_0872Phylogenetic treehttp://doua.prabi.fr/software/seaviewSoftware cataloguehttp://doua.prabi.fr/main/indexGeneral10.1093/molbev/msp25919854763PrimaryIFB ELIXIR-FRInstituteProviderManolo Gouymgouy@biomserv.uni-lyon1.frPersonPrimary contactSWIPETool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs.http://dna.uio.no/swipeswipebiotools:swipe2.0.5Command-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3047Molecular biologyLinuxC++AGPL-3.0MatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_2977Nucleic acid sequencehttps://github.com/torognes/swipeRepositoryhttps://github.com/torognes/swipeSource codehttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-221Citation instructionshttp://dna.uio.no/swipe/General10.1186/1471-2105-12-22121631914PMC3120707PrimaryTorbjørn RognesPersonDeveloperUiOInstituteProvidertorognes@ifi.uio.noPersonPrimary contactrnaSeqMapA library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time.http://bioconductor.org/packages/release/bioc/html/rnaSeqMap.htmlrnaseqmapbiotools:rnaseqmap2.32.0Command-line toolLibraryhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0203Gene expressionLinuxWindowsMacRGPL-2.0BioConductorhttp://edamontology.org/operation_3680RNA-Seq analysishttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://bioconductor/packages/release/bioc/src/contrib/rnaSeqMap_2.32.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/rnaSeqMap.htmlUser manual10.1186/1471-2105-12-20021612622PMC3128033PrimaryMichal Okoniewskimichal@fgcz.ethz.chPersonPrimary contactRbowtieThis package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use QuasR instead of using this package directly.http://bioconductor.org/packages/release/bioc/html/Rbowtie.htmlrbowtiebiotools:rbowtie1.14.0Command-line toolLibraryhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3053GeneticsLinuxWindowsMacArtistic-1.0BioConductorhttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_1957rawhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://bioconductor/packages/release/bioc/src/contrib/Rbowtie_1.14.0.tar.gzSource codehttp://bioconductor.org/packages/release/bioc/html/Rbowtie.htmlUser manual10.1038/nmeth.325225633503PMC4509590OtherMichael Stadlermichael.stadler@fmi.chPersonPrimary contact