pangolinPhylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineageshttps://cov-lineages.org/resources/pangolin.htmlpangolin_cov-lineagesbiotools:pangolin_cov-lineagesv4.0 - v4.3.1Command-line toolhttp://edamontology.org/topic_0781VirologyLinuxMacGPL-3.0COVID-19MatureFree of chargeOpen accessToolshttp://edamontology.org/operation_0499Tree-based sequence alignmenthttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1872Taxonomic classificationhttp://edamontology.org/format_3751DSVhttps://github.com/cov-lineages/pangolinRepository10.1093/ve/veab064Áine O'ToolePersonDeveloperphysherA multi-algorithmic framework for phylogenetic inferencehttps://github.com/4ment/physherphysherbiotools:physher2.0.0Command-line toolhttp://edamontology.org/topic_3293PhylogeneticsMacLinuxCC++GPL-2.0Free of chargeOpen accesshttp://edamontology.org/operation_0547Phylogenetic inference (maximum likelihood and Bayesian methods)http://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newick10.1186/s12862-014-0163-6Primary10.1093/sysbio/syz046UsageMathieu Fourmentmathieu.fourment@uts.edu.auhttps://github.com/4menthttps://orcid.org/0000-0001-8153-9822PersonPrimary contactDeveloperMaintainerSupportSingleMNovelty-inclusive microbial community profiling of shotgun metagenomeshttps://wwood.github.io/singlem/singlembiotools:singlemCommand-line toolhttp://edamontology.org/topic_3174MetagenomicsLinuxPythonGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_3752CSVhttps://wwood.github.io/singlem/GeneralCommand-line optionsInstallation instructions10.1101/2024.01.30.578060KingfisherEasier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.https://github.com/wwood/kingfisher-downloadkingfisherbiotools:kingfisherhttp://edamontology.org/topic_0077Nucleic acidsLinuxMacPythonGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0349Sequence database search (by property)http://edamontology.org/data_2091Accessionhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_3698SRA formathttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAkingfisher get -r ERR1739691 -m ena-ascp aws-http prefetchhttps://wwood.github.io/kingfisher-download/Command-line optionsGeneralInstallation instructionsNetAllergenNetAllergen-1.0 is a predictive model based on the random forest algorithm. It incorporates novel MHC class II presentation propensity features to improve the allergenicity prediction.https://services.healthtech.dtu.dk/services/NetAllergen-1.0/netallergenbiotools:netallergenWeb applicationhttp://edamontology.org/topic_2830Immunoproteins and antigenshttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_0154Small moleculesMacLinuxWindowsFree of chargeOpen accesshttp://edamontology.org/operation_0252Peptide immunogenicity predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0452Indel detectionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA10.1093/BIOADV/VBAD15137901344PMC10603389Carolina Barracarolet@dtu.dkhttps://orcid.org/0000-0002-6836-4906PersonYuchen LiPersonBaCelLoPredictor for the subcellular localization of proteins in eukaryotes.https://busca.biocomp.unibo.it/bacellobacellobiotools:bacello1.0Web applicationhttp://edamontology.org/topic_0140Protein targeting and localisationhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0780Plantshttp://edamontology.org/topic_0621Model organismsLinuxWindowsMacBologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2331HTMLPrediction for the subcellular localizationhttps://busca.biocomp.unibo.it/bacelloGeneral10.1093/bioinformatics/btl22216873501PrimaryELIXIR-ITA-BOLOGNAhttp://biocomp.unibo.itDivisionProviderAndrea Pierleoniandrea@biocomp.unibo.itPersonPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonMaintainerPredGPIPrediction system for GPI-anchored proteins.https://busca.biocomp.unibo.it/predgpipredgpibiotools:predgpi1.0Web applicationhttp://edamontology.org/topic_3542Protein secondary structurehttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacBologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_3351Molecular surface analysishttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2331HTMLPredictionhttps://busca.biocomp.unibo.it/predgpiGeneral10.1186/1471-2105-9-392PrimaryELIXIR-ITA-BOLOGNAInstituteProviderAndrea Pierleoniandrea@biocomp.unibo.itPersonPrimary contactRita Casadiocasadio@biocomp.unibo.itPersonPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonMaintainerDisLocatePrediction of cysteine connectivity patterns in a protein chain.https://busca.biocomp.unibo.it/dislocatedislocatebiotools:dislocate1.0Web applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_3542Protein secondary structureLinuxWindowsMacBologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_1830Free cysteine detectionhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_1829Cysteine bridge detectionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2331HTMLPredictionhttps://busca.biocomp.unibo.it/dislocate/methodGeneral10.1093/bioinformatics/btr38721715467Primary10.1186/1471-2105-14-S1-S1023368835PMC3548674Other10.1007/978-3-642-21946-7_8OtherELIXIR-ITA-BOLOGNAInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttp://biocomp.unibo.it/savojard/https://orcid.org/0000-0002-7359-0633PersonPrimary contactDeveloperMaintainerSChloroPrediction of protein sub-chloroplastinc localization.https://busca.biocomp.unibo.it/schloroschlorobiotools:schloro1Web applicationCommand-line toolhttp://edamontology.org/topic_0140Protein targeting and localisationhttp://edamontology.org/topic_0780Plant biologyLinuxWindowsMacGPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2955Sequence reporthttp://edamontology.org/format_2331HTMLhttps://github.com/BolognaBiocomp/schloroSource codehttps://hub.docker.com/r/bolognabiocomp/schloroContainer filehttps://schloro.biocomp.unibo.it/sclpred/default/indexGeneralhttps://github.com/BolognaBiocomp/schloroCommand-line options10.1093/bioinformatics/btw65628172591PMC5408801PrimaryELIXIR-ITA-BOLOGNAhttp://www.biocomp.unibo.itInstituteMaintainerCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperPrimary contactMaintainerDeepSigPrediction of secretory signal peptides in protein sequenceshttps://busca.biocomp.unibo.it/deepsig/deepsigbiotools:deepsig1.0Web applicationCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacGPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2331HTMLhttps://github.com/BolognaBiocomp/deepsigSource code1.2.5https://hub.docker.com/r/bolognabiocomp/deepsigContainer filehttps://github.com/BolognaBiocomp/deepsigCommand-line options10.1093/bioinformatics/btx81829280997PMC5946842Primary1.0ELIXIR-ITA-BOLOGNAhttp://biocomp.unibo.itInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttp://biocomp.unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contact