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Last ModifiedNameCategoryNotesAuthorURLCitationSourceImageVersionDeveloped ByLicenseLanguage/FrameworkInput FormatOutput FormatDate of Release
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11/13/2023 22:12:19drVMAssembly TooldrVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomeshttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466706/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19GenomeDetective VirusAssembly Toolhttps://www.genomedetective.com/app/typingtool/virus/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19IVAAssembly Toolde-novo assembly, needs to be incorporated in pipeline with host sequence removal, e.g., shiverhttp://sanger-pathogens.github.io/iva/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19IVARAssembly ToolDesigned for mapping-based "assembly" of amplicon sequencing datahttps://github.com/andersen-lab/ivarRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19metaViralSpadesAssembly Toolhttps://academic.oup.com/bioinformatics/article-abstract/36/14/4126/5837667Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19rnaViralSpadesAssembly Toolhttps://www.biorxiv.org/content/10.1101/2020.07.28.224584v1Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19savageAssembly Toolhttps://bitbucket.org/jbaaijens/savage/src/master/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19v-pipeAssembly Toolhttps://github.com/cbg-ethz/V-pipe/tree/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19vicunaAssembly Toolhttps://www.broadinstitute.org/viral-genomics/vicunaRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19VIPAssembly ToolPhage VIrion Protein classification based on chaos game representation and Vision Transformer; Both |
https://github.com/KennthShang/PhaVIP; https://github.com/keylabivdc/VIP/
https://www.nature.com/articles/srep23774Rob Edwards' Viral Bioinfo Tools; Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19viral-ngsAssembly Toolhttps://viral-ngs.readthedocs.io/en/latest/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19VirusTAPAssembly ToolWEBSERVER - No option to registerhttps://gph.niid.go.jp/virustap/system_inRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19
Choice of assembly software has a critical impact on virome characterisation
BenchmarkPhage assembly benchmarkhttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0626-5/tables/1Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19
Evaluation of computational phage detection tools for metagenomic datasets
BioinformaticsPhage detection in metagenomes tools benchmarkhttps://www.frontiersin.org/articles/10.3389/fmicb.2023.1078760/fullRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19MaGplotRCRISPRVirus | CRISPR Screens |
https://github.com/alematia/MaGplotR
https://www.biorxiv.org/content/10.1101/2023.01.12.523725v1Rob Edwards' Viral Bioinfo Tools20230112
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11/13/2023 22:12:19SpacePHARERCRISPRPhage | CRISPR Spacer Phage-Host Pair Finder |spacepharer.soedinglab.orghttps://www.biorxiv.org/content/10.1101/2020.05.15.090266v1Rob Edwards' Viral Bioinfo Tools20220906
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11/13/2023 22:12:19BVBRC
Cyberinfrastructure-supported virus tools
Both | Website |https://bitbucket.org/srouxjgi/iphophttp://bvbrc.orgRob Edwards' Viral Bioinfo ToolsActively developed
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11/13/2023 22:12:19iVirus 2.0
Cyberinfrastructure-supported virus tools
Phage | integrating iVirus apps on CyVerse and KBase |CyVerse ( KBase (https://www.nature.com/articles/s43705-021-00083-3
http://tinyurl.com/4ndkt4n2),
https://kbase.us/applist/)		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PhageAI
Data repository, life cycle, taxonomy and proteins structure prediction, phage similarity, phage annotation
Phage | NLP, ML |https://www.biorxiv.org/content/10.1101/2020.07.11.198606v1
https://app.phage.ai/		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19DePPDepolymerase finderPhagehttps://timskvortsov.github.io/WebDePP/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PhageDPODepolymerase finderPhage | SVM and ANNbit.ly/phagedpoRob Edwards' Viral Bioinfo Tools2022
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11/13/2023 22:12:19OLGenieDiversity and selection analysisBoth | Program for estimating dN/dS in overlapping genes (OLGs); inferring purifying selection in alternative reading frames; intrahost; within-host; evolution; selection; nucleotide diversity |
https://github.com/chasewnelson/OLGenie
https://academic.oup.com/mbe/article/37/8/2440/5815567Rob Edwards' Viral Bioinfo Tools20221202
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11/13/2023 22:12:19SNPGenieDiversity and selection analysisBoth | Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data; intrahost; within-host; evolution; selection; nucleotide diversity |
https://github.com/chasewnelson/snpgenie
https://academic.oup.com/bioinformatics/article/31/22/3709/241742Rob Edwards' Viral Bioinfo Tools20230822
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11/13/2023 22:12:19VCFgenieDiversity and selection analysisBoth | Program for reproducibly filtering VCF files and eliminating false positive variants; intrahost; within-host; evolution; selection; nucleotide diversity | In revisionhttps://github.com/chasewnelson/VCFgenieRob Edwards' Viral Bioinfo Tools20220825
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11/13/2023 22:12:19VIPERAEvolutionary analysisVirus | Phylogenetic and population genetics-based analysis of intra-patient SARS-CoV-2 |
https://github.com/PathoGenOmics-Lab/VIPERA
https://doi.org/10.1101/2023.10.24.561010Rob Edwards' Viral Bioinfo Tools20231108
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11/13/2023 22:12:19MetaCerberusGenome and virome annotationBoth | HMM-based with Ray MPP |
https://github.com/raw-lab/MetaCerberus
https://www.biorxiv.org/content/10.1101/2023.08.10.552700v1Rob Edwards' Viral Bioinfo Tools2023
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11/13/2023 22:12:19DRAMvGenome annnotationPhage | Distilling and refining annotation of metabolism |
https://github.com/WrightonLabCSU/DRAM
https://academic.oup.com/nar/article/48/16/8883/5884738Rob Edwards' Viral Bioinfo Tools2023
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11/13/2023 22:12:19PhANNsGenome annnotationPhage |PhANNshttps://journals.plos.org/ploscompbiol/article/authors?id=10.1371/journal.pcbi.1007845Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PharokkaGenome annnotationPhage |
https://github.com/gbouras13/pharokka
https://doi.org/10.1093/bioinformatics/btac776Rob Edwards' Viral Bioinfo Tools20230124
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11/13/2023 22:12:19coronaSPAdesGenome assemblyBoth | HMM-synteny guided assembly (works for all viruses) |
https://github.com/ablab/spades/tree/metaviral_publication
https://academic.oup.com/bioinformatics/article/38/1/1/6354349Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19metaviralSPAdesGenome assemblyBoth | MetaviralSPAdes: assembly of viruses from metagenomic data | Bioinformatics | Oxford Academichttps://github.com/ablab/spades/tree/metaviral_publicationRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19mulitPHATEGenome comparisonPhagehttps://github.com/carolzhou/multiPhATERob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PhageCloudsGenome comparisonPhage | network graphs |https://doi.org/10.1089/phage.2021.0008Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19CheckVGenome completenessBoth |; CheckV: assessing the quality of metagenome-assembled viral genomes
https://bitbucket.org/berkeleylab/checkv/src/master/
https://www.biorxiv.org/content/10.1101/2020.05.06.081778v1Rob Edwards' Viral Bioinfo Tools20220906
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11/13/2023 22:12:19viralCompleteGenome completenessBothhttps://github.com/ablab/viralComplete/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19viralVerifyGenome completenessBothhttps://github.com/ablab/viralVerify/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19
BacteriophageHostPrediction
Host predictionPhage |
https://github.com/dimiboeckaerts/BacteriophageHostPrediction
https://www.nature.com/articles/s41598-021-81063-4Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19CHERRYHost predictionPhage |
https://github.com/KennthShang/CHERRY
https://academic.oup.com/bib/article/23/5/bbac182/6589865Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19CrisprOpenDBHost predictionPhage |
https://github.com/edzuf/CrisprOpenDB
https://doi.org/10.1093/nar/gkab133Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19DeePaCHost predictionBoth | CNN, ResNet, Shapley values (interpretability) |https://academic.oup.com/nargab/article/3/1/lqab004/6125551,
https://academic.oup.com/bib/article/22/6/bbab269/6326527,
https://academic.oup.com/bioinformatics/article/38/Supplement_2/ii168/6702016
https://gitlab.com/dacs-hpi/deepac		Rob Edwards' Viral Bioinfo Tools20221216
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11/13/2023 22:12:19DeePaC-LiveHost predictionBoth | ResNet |https://academic.oup.com/bib/article/22/6/bbab269/6326527
https://gitlab.com/dacs-hpi/deepac-live		Rob Edwards' Viral Bioinfo Tools20210123
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11/13/2023 22:12:19DeepHostHost predictionPhage | CNN |
**Description:**



DeepHost is a phage host prediction tool.; DeepHost is a phage host prediction tool.
https://github.com/deepomicslab/DeepHost
https://github.com/deepomicslab/DeepHost; https://github.com/deepomicslab/DeepHost
https://academic.oup.com/bib/article-abstract/23/1/bbab385/6374063?redirectedFrom=fulltextRob Edwards' Viral Bioinfo Tools; Phage Kitchen20220804
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11/13/2023 22:12:19HostGHost predictionPhage | GCN |
https://github.com/KennthShang/HostG
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01180-4Rob Edwards' Viral Bioinfo Tools20220316
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11/13/2023 22:12:19HostPhinderHost predictionPhage | k-mers |https://github.com/julvi/HostPhinderhttps://pubmed.ncbi.nlm.nih.gov/27153081/Rob Edwards' Viral Bioinfo Tools20200902
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11/13/2023 22:12:19INFH-VHHost predictionPhage |https://github.com/liudan111/ILMF-VHhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3082-0Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19iPHoPHost predictionPhage |https://www.biorxiv.org/content/10.1101/2022.07.28.501908v1.abstractRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19MVPHost predictionBoth |https://academic.oup.com/nar/article/46/D1/D700/4643372?login=true
http://mvp.medgenius.info/home		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PHERIHost predictionPhage | PHERIhttps://github.com/andynet/pheriRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PHIAFHost predictionPhage | GAN |
https://github.com/BioMedicalBigDataMiningLab/PHIAF
https://academic.oup.com/bib/article-abstract/23/1/bbab348/6362109Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PHISDetectorHost predictionPhagehttp://www.microbiome-bigdata.com/PHISDetector/index/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PHISTHost predictionPhage | k-mers |https://github.com/refresh-bio/phisthttps://academic.oup.com/bioinformatics/article/38/5/1447/6460800Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PHPHost predictionPhagehttps://github.com/congyulu-bioinfo/PHPRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PredPHIHost predictionPhagehttps://github.com/xialab-ahu/PredPHIRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19RaFaHHost predictionPhage |https://www.sciencedirect.com/science/article/pii/S2666389921001008
https://sourceforge.net/projects/rafah/		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19vHulkHost predictionPhage |
**Description:**




**Phage Host Prediction using high level features and neural networks**

Metagenomics and sequencing techniques have greatly improved in these last five years and, as a consequence, the amount of data from microbial communities is astronomic. An import part of the microbial community are phages, which have their own ecological roles in the environment. Besides that, they have also been given a possible human relevant (clinical) role as terminators of multidrug resistant bacterial infections. A lot of basic research still need to be done in the Phage therapy field, and part of this research involves gathering knowledge from new phages present in the environment as well as about their relationship with clinical relevant bacterial pathogens.

Having this scenario in mind, we have developed vHULK. A user-friendly tool for prediction of phage hosts given their complete or partial genome in FASTA format. Our tool outputs an ensemble prediction at the genus or species level based on scores of four different neural network models. Each model was trained with more than 4,000 genomes whose phage-host relationship was known. v.HULK also outputs a mesure of entropy for each final prediction, which we have demonstrated to be correlated with prediction's accuracy. The user might understand this value as additional information of how certain v.HULK is about a particular prediction. We also suspect that phages with higher entropy values may have a broad host-range. But that hypothesis is to be tested later. Accuracy results in test datasets were >99% for predictions at the genus level and >98% at the species level. vHULK currently supports predictions for 52 different prokaryotic host species and 61 different genera.
nan
https://github.com/LaboratorioBioinformatica/vHULK
https://www.biorxiv.org/content/10.1101/2020.12.06.413476v1
https://www.biorxiv.org/content/10.1101/2020.12.06.413476v1.full		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19VIDHOPHost predictionBoth | Deep learning |https://github.com/flomock/vidhophttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454304/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19VirHostMatcherHost predictionPhage | oligonucleotide frequency based distance and dissimilarity measures |
https://github.com/jessieren/VirHostMatcher
https://pubmed.ncbi.nlm.nih.gov/27899557/Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19VirHostMatcher-NetHost predictionVirus |
**Description:**




Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus–prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures (⁠s∗2 and WIsH). Evaluation of this method on a benchmark set of 1462 known virus–prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16–27% and 6–10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, and two metagenomic virus datasets: marine viruses and viral contigs recovered from globally distributed, diverse habitats. Host predictions were frequently consistent with those of previous studies, but more importantly, this new tool made many more confident predictions than previous tools, up to nearly 3-fold more (n > 27 000), greatly expanding the diversity of known virus–host interactions.; Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus‚Äìprokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures (‚ņs‚àó2 and WIsH). Evaluation of this method on a benchmark set of 1462 known virus‚Äìprokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16‚Äì27% and 6‚Äì10% improvement, respectively, over previous single-feature prediction approaches. We applied our host prediction tool to crAssphage, a human gut phage, and two metagenomic virus datasets: marine viruses and viral contigs recovered from globally distributed, diverse habitats. Host predictions were frequently consistent with those of previous studies, but more importantly, this new tool made many more confident predictions than previous tools, up to nearly 3-fold more (n > 27 000), greatly expanding the diversity of known virus‚Äìhost interactions.
https://github.com/WeiliWw/VirHostMatcher-Net
https://github.com/WeiliWw/VirHostMatcher-Net; https://github.com/WeiliWw/VirHostMatcher-Net
https://academic.oup.com/nargab/article/2/2/lqaa044/5861484?login=true
https://academic.oup.com/nargab/article/2/2/lqaa044/5861484; https://academic.oup.com/nargab/article/2/2/lqaa044/5861484
Rob Edwards' Viral Bioinfo Tools; Phage Kitchen
https://trello.com/1/cards/61948b43aa653c636dd10832/attachments/61ba828f6d63dd22924262d0/download/image.png
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11/13/2023 22:12:19VirMatcherHost predictionPhage | Leveraging multiple methods and assigning a confidence score |
https://bitbucket.org/MAVERICLab/virmatcher/src/master/
https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(20)30456-XRob Edwards' Viral Bioinfo Tools20220429
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11/13/2023 22:12:19Virus Host DBHost predictionBoth |https://pubmed.ncbi.nlm.nih.gov/26938550/
https://www.genome.jp/virushostdb/		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19Virus Host PredictHost predictionBothhttps://github.com/youngfran/virus_host_predictRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19WIsHHost predictionPhage |https://github.com/soedinglab/WIsHhttps://academic.oup.com/bioinformatics/article/33/19/3113/3964377#:~:text=WIsH%20predicts%20prokaryotic%20hosts%20of,3%20kbp%2Dlong%20phage%20contigs.Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19ReadItAndKeepHost Removal Toolhttps://github.com/GenomePathogenAnalysisService/read-it-and-keepRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19shiverHost Removal Toolhttps://github.com/ChrisHIV/shiverRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19DRADIdentify Integrated VirusesPhage | Dinucleotide Relative Abundance difference |Does not exist any morehttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001193Rob Edwards' Viral Bioinfo ToolsNone
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11/13/2023 22:12:19geNomadIdentify Integrated VirusesBothhttps://github.com/apcamargo/genomadRob Edwards' Viral Bioinfo Tools20221015
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11/13/2023 22:12:19hafeZIdentify Integrated VirusesPhage | Readmapping |https://github.com/Chrisjrt/hafeZhttps://www.biorxiv.org/content/10.1101/2021.07.21.453177v1Rob Edwards' Viral Bioinfo Tools20211004
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11/13/2023 22:12:19LysoPhDIdentify Integrated VirusesPhage |No code availablehttps://ieeexplore.ieee.org/document/8983280Rob Edwards' Viral Bioinfo ToolsNone
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11/13/2023 22:12:19phage_finderIdentify Integrated VirusesPhage |https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635311/
http://phage-finder.sourceforge.net/		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19phageboostIdentify Integrated VirusesPhage | boost ml |https://www.biorxiv.org/content/10.1101/2020.08.09.243022v1
http://phageboost.ml		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PhageWebIdentify Integrated VirusesPhage |https://www.frontiersin.org/articles/10.3389/fgene.2018.00644/full
http://computationalbiology.ufpa.br/phageweb/		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PHASTERIdentify Integrated Viruses
Phage |
**Description:**




PHASTER (PHAge Search Tool Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. While the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3X faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X faster than PHAST. Likewise, the addition of more than 120 CPUs to the PHASTER compute cluster have greatly reduced processing times. PHASTER can now process a typical bacterial genome in 3 minutes from the raw sequence alone, or in 1.5 minutes when given a pre-annotated GenBank file. A number of other optimizations have been implemented, including automated algorithms to reduce the size and redundancy of PHASTER’s databases, improvements in handling multiple (metagenomic) queries and high user traffic, and the ability to perform automated look-ups against >14,000 previously PHAST/PHASTER annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). PHASTER’s web interface has also been entirely rewritten. A new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust, and user-friendly.; PHASTER (PHAge Search Tool Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. While the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3X faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X faster than PHAST. Likewise, the addition of more than 120 CPUs to the PHASTER compute cluster have greatly reduced processing times. PHASTER can now process a typical bacterial genome in 3 minutes from the raw sequence alone, or in 1.5 minutes when given a pre-annotated GenBank file. A number of other optimizations have been implemented, including automated algorithms to reduce the size and redundancy of PHASTER‚Äôs databases, improvements in handling multiple (metagenomic) queries and high user traffic, and the ability to perform automated look-ups against >14,000 previously PHAST/PHASTER annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). PHASTER‚Äôs web interface has also been entirely rewritten. A new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust, and user-friendly.
https://pubmed.ncbi.nlm.nih.gov/27141966/
https://phaster.ca/
https://phaster.ca/
http://www.ncbi.nlm.nih.gov/pubmed/27141966; http://www.ncbi.nlm.nih.gov/pubmed/27141966
https://phaster.ca/		Rob Edwards' Viral Bioinfo Tools; Phage Kitchen
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11/13/2023 22:12:19PhigaroIdentify Integrated VirusesPhage |; Phigaro: high throughput prophage sequence annotationhttps://github.com/bobeobibo/phigarohttps://www.biorxiv.org/content/10.1101/598243v1Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19PhiSpyIdentify Integrated VirusesPhage | PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies - PMChttps://github.com/linsalrob/PhiSpyRob Edwards' Viral Bioinfo Tools20220202
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11/13/2023 22:12:19Prophage HunterIdentify Integrated VirusesPhage | logistic regression |https://academic.oup.com/nar/article/47/W1/W74/5494712
https://pro-hunter.bgi.com/		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19ProphetIdentify Integrated VirusesPhage |https://github.com/jaumlrc/ProphEThttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223364Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19ProphinderIdentify Integrated VirusesPhage |https://academic.oup.com/bioinformatics/article/24/6/863/194494
http://aclame.ulb.ac.be/Tools/Prophinder/		Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19VAPiDIdentify Integrated VirusesVirus |https://github.com/rcs333/VAPiDhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2606-yRob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19viralintegrationIdentify Integrated VirusesVirus | Nextflow pipelinehttps://github.com/nf-core/viralintegrationRob Edwards' Viral Bioinfo Tools2023
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11/13/2023 22:12:19BACPHLIPLifestyle classificationPhage | Random Forest classifier |
**Description:**



Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages are capable of a latent phase of infection within a host cell (lysogenic cycle), whereas virulent phages directly replicate and lyse host cells upon infection (lytic cycle). Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution. Here, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier that was trained on a dataset of 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98% greatly exceeding that of the previously existing tools (79%). BACPHLIP is freely available on GitHub
(
and the code used to build and test the classifier is provided in a separate repository
(
for users wishing to interrogate and re-train the underlying classification model.; Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages are capable of a latent phase of infection within a host cell (lysogenic cycle), whereas virulent phages directly replicate and lyse host cells upon infection (lytic cycle). Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution. Here, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier that was trained on a dataset of 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98% greatly exceeding that of the previously existing tools (79%). BACPHLIP is freely available on GitHub
(
and the code used to build and test the classifier is provided in a separate repository
(
for users wishing to interrogate and re-train the underlying classification model.
https://github.com/adamhockenberry/bacphlip
https://github.com/adamhockenberry/bacphlip)
https://github.com/adamhockenberry/bacphlip-model-dev); https://github.com/adamhockenberry/bacphlip)
https://github.com/adamhockenberry/bacphlip-model-dev)
https://pubmed.ncbi.nlm.nih.gov/33996289/
https://pubmed.ncbi.nlm.nih.gov/33996289/; https://pubmed.ncbi.nlm.nih.gov/33996289/		Rob Edwards' Viral Bioinfo Tools; Phage Kitchen20210128
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11/13/2023 22:12:19PHACTSLifestyle classificationPhage |
**Description:**



PHACTS-0.3.tar.gz

**Abstract**
*Motivation*: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques. Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore, a computational method that utilizes the sequence data of phage genomes is needed.

*Results*: Phage Classification Tool Set (PHACTS) utilizes a novel similarity algorithm and a supervised Random Forest classifier to make a prediction whether the lifestyle of a phage, described by its proteome, is virulent or temperate. The similarity algorithm creates a training set from phages with known lifestyles and along with the lifestyle annotation, trains a Random Forest to classify the lifestyle of a phage. PHACTS predictions are shown to have a 99% precision rate.

*Availability and implementation*: PHACTS was implemented in the PERL programming language and utilizes the FASTA program (Pearson and Lipman, 1988) and the R programming language library 'Random Forest' (Liaw and Weiner, 2010). The PHACTS software is open source and is available as downloadable stand-alone version or can be accessed online as a user-friendly web interface. The source code, help files and online version are available at; PHACTS-0.3.tar.gz

Abstract
Motivation: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques. Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore, a computational method that utilizes the sequence data of phage genomes is needed.

Results: Phage Classification Tool Set (PHACTS) utilizes a novel similarity algorithm and a supervised Random Forest classifier to make a prediction whether the lifestyle of a phage, described by its proteome, is virulent or temperate. The similarity algorithm creates a training set from phages with known lifestyles and along with the lifestyle annotation, trains a Random Forest to classify the lifestyle of a phage. PHACTS predictions are shown to have a 99% precision rate.

Availability and implementation: PHACTS was implemented in the PERL programming language and utilizes the FASTA program (Pearson and Lipman, 1988) and the R programming language library 'Random Forest' (Liaw and Weiner, 2010). The PHACTS software is open source and is available as downloadable stand-alone version or can be accessed online as a user-friendly web interface. The source code, help files and online version are available at		https://pubmed.ncbi.nlm.nih.gov/22238260/
https://pubmed.ncbi.nlm.nih.gov/22238260/
https://edwards.sdsu.edu/PHACTS/
https://edwards.sdsu.edu/PHACTS/PHACTS-0.3.tar.gz
http://www.phantome.org/PHACTS/.; https://edwards.sdsu.edu/PHACTS/
https://edwards.sdsu.edu/PHACTS/PHACTS-0.3.tar.gz
http://www.phantome.org/PHACTS/.
https://pubmed.ncbi.nlm.nih.gov/22238260/		Rob Edwards' Viral Bioinfo Tools; Phage Kitchen
83
11/13/2023 22:12:19ViralMSAMultiple Sequence AlignmentVirus | Python script that wraps around read mappers (e.g. Minimap2) |https://github.com/niemasd/ViralMSAhttps://doi.org/10.1093/bioinformatics/btaa743Rob Edwards' Viral Bioinfo ToolsActively developed
84
11/13/2023 22:12:19PhanotatePhage genesPhage |
**Description:**




PHANOTATE is a tool to annotate phage genomes. It uses the assumption that non-coding bases in a phage genome is disadvantageous, and then populates a weighted graph to find the optimal path through the six frames of the DNA where open reading frames are beneficial paths, while gaps and overlaps are penalized paths.
https://github.com/deprekate/PHANOTATE
https://github.com/deprekate/PHANOTATE
https://academic.oup.com/bioinformatics/article/35/22/4537/5480131
https://academic.oup.com/bioinformatics/article/35/22/4537/5480131		Rob Edwards' Viral Bioinfo Tools
85
11/13/2023 22:12:19PHROGsPhage genesPhage |https://academic.oup.com/nargab/article/3/3/lqab067/6342220Rob Edwards' Viral Bioinfo Tools
86
11/13/2023 22:12:19PHREDPhage receptorsPhage |No longer availablehttps://academic.oup.com/femsle/article/363/4/fnw002/1845417Rob Edwards' Viral Bioinfo Tools
87
11/13/2023 22:12:19PlaqueSizeToolPlaque size calculationPhage | Based on the optimized Computer Vision library |
https://github.com/ellinium/plaque_size_tool
https://www.sciencedirect.com/science/article/pii/S004268222100115X?via%3DihubRob Edwards' Viral Bioinfo Tools2022
88
11/13/2023 22:12:19
PlaqueSizeTool (colab version)
Plaque size calculationPhage | Based on the optimized Computer Vision library |https://www.sciencedirect.com/science/article/pii/S004268222100115X?via%3Dihub
https://colab.research.google.com/drive/1HJe8V26l7n82zX8vJ7bO5C8-xrs_aWuq?usp=sharing		Rob Edwards' Viral Bioinfo Tools2023
89
11/13/2023 22:12:19PhageTerm
Predicting phage packaging mechanism
Phage | Read mapping |https://www.nature.com/articles/s41598-017-07910-5
https://gitlab.pasteur.fr/vlegrand/ptv/-/releases		Rob Edwards' Viral Bioinfo Tools
90
11/13/2023 22:12:19
Virus-Host Interaction Predictor (VHIP)
PredictionG. Eric Bastien and colleagues have developed a [machine learning model called Virus-Host Interaction Predictor (VHIP)]( to predict virus-host interactions and reconstruct complex virus-host networks in natural systems.G. Eric Bastien and othershttps://www.biorxiv.org/content/10.1101/2023.11.03.565433v1)
https://www.biorxiv.org/content/10.1101/2023.11.03.565433v1		Rob Edwards' Viral Bioinfo Tools
91
11/13/2023 22:12:19PhagePromoterPromotersPhage | artificial neural network (ANN), support vector machines (SVM) |
https://github.com/martaS95/PhagePromoter
https://academic.oup.com/bioinformatics/article/35/24/5301/5540317Rob Edwards' Viral Bioinfo Tools
92
11/13/2023 22:12:19DeepVHPPIProtein:Protein InteractionsVirus |https://github.com/QData/DeepVHPPIhttps://dl.acm.org/doi/abs/10.1145/3459930.3469527Rob Edwards' Viral Bioinfo Tools
93
11/13/2023 22:12:19PhageRBPdetectRBPPhage | HMMs & machine learning |https://www.mdpi.com/1999-4915/14/6/1329Rob Edwards' Viral Bioinfo Tools
94
11/13/2023 22:12:19
EVBC Virus Bioinformatics Tools
ResourceA collection of useful tools in Virus Bioinformatics curated by the European Virus Bioinformatics Center. Please note, that the EVBC is not maintaining the toolsEVBChttps://evirusbioinfc.notion.site/evirusbioinfc/18e21bc49827484b8a2f84463cb40b8d?v=92e7eb6703be4720abf17a901bc9a947Rob Edwards' Viral Bioinfo Tools
95
11/13/2023 22:12:19MGE detection toolsResourceA collection of bacteria/virus toolshttps://docs.google.com/spreadsheets/d/1dL5o524IX_-hJB6iYV1FB4QrK_U5KgFcfM4rZDZV_Dw/edit#gid=0Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19Phage KitchenResourceComparison and categorization of MANY phage bioinformatics toolsNouri Ben Zakourhttps://github.com/nbenzakour/phage-kitchenNouri Ben Zakour
97
11/13/2023 22:12:19Phage prediction toolsResourceGithub repo accompanying paper: "Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data" by Siu Fung Stanley Ho, Nicole E. Wheeler, Andrew D. Millard & Willem van Schaik (
https://github.com/sxh1136/Phage_tools
https://doi.org/10.1186/s40168-023-01533-x)Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19
Rob Edwards' Viral Bioinformatics Tools
ResourcePeriodically updated open spreadsheet of bioinformatics tools; owned by Rob EdwardsRob Edwardshttps://docs.google.com/spreadsheets/d/1ClNgip08olKK-oBMMlPHBwIcilqSxsan8MEaYphUei4/edit#gid=1636291468Rob Edwards' Viral Bioinfo Tools
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11/13/2023 22:12:19TE Hub Repeat DatabasesResourceA list of databases for the storage of sequences and metadata associated with repetitive, mobile and selfish DNATyler Elliotthttps://tehub.org/en/resources/repeat_databasesRob Edwards' Viral Bioinfo Tools
100
11/13/2023 22:12:19
Testing (5) Prophage finding tools
ResourceComparison of five (text updated with 5th tool) prophage finding tools for bacterial genomics — Phispy, VirSorter, Phigaro, ProphET, PHASTERhttps://nickp60.github.io/weird_one_offs/testing_3_prophage_finders/Rob Edwards' Viral Bioinfo Tools