| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | Timestamp | Tool name | Category | Is this tool designed for: | What kind of methods does this tool use? | Citation | Repository | How can you install this tool? | What is the size of the database, if appropriate? | Does this run on: | ||||||
2 | 18/07/2024 16:02:36 | Metapop | Other .... | Both | Visualising microdiversity | https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01231-0 | https://github.com/metaGmetapop/metapop | conda, pip, source | Laptop, Desktop | |||||||
3 | 18/07/2024 16:55:22 | ProphageDB | Identify Integrated Viruses | Phages | https://doi.org/10.1101/2024.07.11.603044 | https://github.com/AnantharamanLab/Prophage-DB | ||||||||||
4 | BACPHLIP | Lifestyle classification | Phage | Random Forest classifier | https://pubmed.ncbi.nlm.nih.gov/33996289/ | https://github.com/adamhockenberry/bacphlip | ||||||||||
5 | BacteriophageHostPrediction | Host prediction | Phage | https://www.nature.com/articles/s41598-021-81063-4 | https://github.com/dimiboeckaerts/BacteriophageHostPrediction | |||||||||||
6 | BERTax | Virus taxonomy | Both | https://www.pnas.org/doi/full/10.1073/pnas.2122636119 | https://github.com/f-kretschmer/bertax | |||||||||||
7 | BVBRC | Cyberinfrastructure virus tools | Both | Website | http://bvbrc.org | https://bitbucket.org/srouxjgi/iphop | ||||||||||
8 | Cenote-Taker2 | Virus identification in metagenomes | Both | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7816666/pdf/veaa100.pdf | https://github.com/mtisza1/Cenote-Taker2 | |||||||||||
9 | Cenote-Taker3 | Virus identification in metagenomes | Both | Hallmark gene discovery, gene annotation, flanking host gene removal | https://github.com/mtisza1/Cenote-Taker3 | |||||||||||
10 | CheckV | Genome completeness | Both | https://www.biorxiv.org/content/10.1101/2020.05.06.081778v1 | https://bitbucket.org/berkeleylab/checkv/src/master/ | |||||||||||
11 | CHERRY | Host prediction | Phage | https://academic.oup.com/bib/article/23/5/bbac182/6589865 | https://github.com/KennthShang/CHERRY | |||||||||||
12 | CHVD | Sequence Database | Both | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201803/ | https://zenodo.org/record/4498884#.Y2Q9sHZBxD8 | |||||||||||
13 | Classiphages 2.0 | Virus taxonomy | Phage | ANN | https://www.biorxiv.org/content/10.1101/558171v1 | No code available | ||||||||||
14 | COBRA | Viral strain reconstruction | Virus | contig overlaps | https://www.nature.com/articles/s41564-023-01598-2 | https://github.com/linxingchen/cobra | ||||||||||
15 | CoCoNet | Virus identification in metagenomes | Virus | Neural networks | https://academic.oup.com/bioinformatics/article/37/18/2803/6211156 | https://github.com/Puumanamana/CoCoNet | ||||||||||
16 | coronaSPAdes | Genome assembly | Both | HMM-synteny guided assembly (works for all viruses) | https://academic.oup.com/bioinformatics/article/38/1/1/6354349 | https://github.com/ablab/spades/tree/metaviral_publication | ||||||||||
17 | crassus | Virus identification in metagenomes | Phage | snakemake workflow | https://github.com/dcarrillox/CrassUS | |||||||||||
18 | CrisprOpenDB | Host prediction | Phage | https://doi.org/10.1093/nar/gkab133 | https://github.com/edzuf/CrisprOpenDB | |||||||||||
19 | DBSCAN-SWA | Virus identification in metagenomes | Phage | DBSCAN | https://www.frontiersin.org/articles/10.3389/fgene.2022.885048/full | https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/. | ||||||||||
20 | Deep6 | Virus identification in metagenomes | Both | Machine Learning | https://journals.asm.org/doi/10.1128/mra.01079-22 | https://github.com/janfelix/Deep6 | ||||||||||
21 | DeePaC | Host prediction | Both | 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 | ||||||||||
22 | DeePaC-Live | Host prediction | Both | ResNet | https://academic.oup.com/bib/article/22/6/bbab269/6326527 | https://gitlab.com/dacs-hpi/deepac-live | ||||||||||
23 | DeepHost | Host prediction | Phage | CNN | https://academic.oup.com/bib/article-abstract/23/1/bbab385/6374063?redirectedFrom=fulltext | https://github.com/deepomicslab/DeepHost | ||||||||||
24 | DeepVHPPI | Protein:Protein Interactions | Virus | https://dl.acm.org/doi/abs/10.1145/3459930.3469527 | https://github.com/QData/DeepVHPPI | |||||||||||
25 | DeepVirFinder | Virus identification in metagenomes | Both | neural network | https://arxiv.org/pdf/1806.07810.pdf | https://github.com/jessieren/DeepVirFinder | ||||||||||
26 | DePhT | Virus identification in metagenomes | Phage | https://academic.oup.com/nar/article/50/13/e75/6572362 | https://github.com/chg60/DEPhT | |||||||||||
27 | DePP | Depolymerase finder | Phage | https://timskvortsov.github.io/WebDePP/ | ||||||||||||
28 | DRAD | Identify Integrated Viruses | Phage | Dinucleotide Relative Abundance difference | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001193 | Does not exist any more | ||||||||||
29 | DRAMv | Genome annotation | Phage | Distilling and refining annotation of metabolism | https://academic.oup.com/nar/article/48/16/8883/5884738 | https://github.com/WrightonLabCSU/DRAM | ||||||||||
30 | Earth Virome | Sequence Database | Both | https://www.nature.com/articles/nprot.2017.063 | https://portal.nersc.gov/dna/microbial/prokpubs/EarthVirome_DP/ | |||||||||||
31 | efam | Viral orthologous groups | Both | Concensus viral identification, network-based clustering, metaproteomics | https://academic.oup.com/bioinformatics/article/37/22/4202/6300514 | https://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/Zayed_efam_2020.1 | ||||||||||
32 | FastViromeExplorer | Virus identification in metagenomes | Both | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768174/ | https://code.vt.edu/saima5/FastViromeExplorer | |||||||||||
33 | FAVITES | Simulate networks | Both | Simulate contact networks, transmission networks, phylogenies, and sequences | https://doi.org/10.1093/bioinformatics/bty921 | https://github.com/niemasd/FAVITES | ||||||||||
34 | FAVITES-Lite | Simulate networks | Both | Simulate contact networks, transmission networks, phylogenies, and sequences | TBD | https://github.com/niemasd/FAVITES-Lite | ||||||||||
35 | geNomad | Identify Integrated Viruses | Both | https://github.com/apcamargo/genomad | ||||||||||||
36 | GenomePeek | Virus identification in metagenomes | Phage | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476108/ | ||||||||||||
37 | GOV-RNA | Sequence Database | Both | RNA viruses from the Global Ocean | https://www.science.org/doi/abs/10.1126/science.abm5847 | https://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/ZayedWainainaDominguez-Huerta_RNAevolution_Dec2021 | ||||||||||
38 | GOV2.0 | Sequence Database | Both | DNA viruses from the Global Ocean | https://www.cell.com/cell/fulltext/S0092-8674(19)30341-1 | https://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/GOV2.0 | ||||||||||
39 | GPDB | Sequence Database | Both | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7895897/?report=reader | http://ftp.ebi.ac.uk/pub/databases/metagenomics/genome_sets/gut_phage_database/ | |||||||||||
40 | GraViTy | Virus taxonomy | Both | HMMs and genome organisation models | https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0422-7 | https://github.com/PAiewsakun/GRAViTy | ||||||||||
41 | GVD | Sequence Database | Both | https://www.sciencedirect.com/science/article/pii/S193131282030456X | https://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/Gregory_and_Zablocki_GVD_Jul2020 | |||||||||||
42 | hafeZ | Identify Integrated Viruses | Phage | Readmapping | https://www.biorxiv.org/content/10.1101/2021.07.21.453177v1 | https://github.com/Chrisjrt/hafeZ | ||||||||||
43 | hecatomb | Virus identification in metagenomes | Both | https://www.biorxiv.org/content/10.1101/2022.05.15.492003v2 | https://github.com/shandley/hecatomb | |||||||||||
44 | HoloVir | Virus identification in metagenomes | Both | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899465/ | https://github.com/plaffy/HoloVir | |||||||||||
45 | HostG | Host prediction | Phage | GCN | https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01180-4 | https://github.com/KennthShang/HostG | ||||||||||
46 | HostPhinder | Host prediction | Phage | k-mers | https://pubmed.ncbi.nlm.nih.gov/27153081/ | https://github.com/julvi/HostPhinder | ||||||||||
47 | INFH-VH | Host prediction | Phage | https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3082-0 | https://github.com/liudan111/ILMF-VH | |||||||||||
48 | INHERIT | Virus identification in metagenomes | Phage | Embedding (BERT) | https://academic.oup.com/bioinformatics/article/38/18/4264/6654586 | https://github.com/Celestial-Bai/INHERIT | ||||||||||
49 | INSaFLU-TELEVIR | Virus identification in metagenomes | Virus | https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-024-01334-3 | https://github.com/INSaFLU/INSaFLU | |||||||||||
50 | iPHoP | Host prediction | Phage | https://www.biorxiv.org/content/10.1101/2022.07.28.501908v1.abstract | ||||||||||||
51 | isling | Virus identification in metagenomes | Virus | Split read alignment | https://www.sciencedirect.com/science/article/pii/S0022283621006458 | https://github.com/szsctt/intvi_other-tools | ||||||||||
52 | iVirus 2.0 | Cyberinfrastructure virus tools | Phage | integrating iVirus apps on CyVerse and KBase | https://www.nature.com/articles/s43705-021-00083-3 | CyVerse (http://tinyurl.com/4ndkt4n2), KBase (https://kbase.us/applist/) | ||||||||||
53 | Jaeger | Virus identification in metagenomes | Phage | https://github.com/Yasas1994/Jaeger | ||||||||||||
54 | Jovian | Virus identification in metagenomes | Virus | https://github.com/DennisSchmitz/Jovian | ||||||||||||
55 | KEGG Virus | Sequence Database | Both | https://www.genome.jp/kegg/genome/virus.html | ||||||||||||
56 | LazyPipe | Virus identification in metagenomes | Both | https://academic.oup.com/ve/article/6/2/veaa091/6017186?login=false | https://www.helsinki.fi/en/projects/lazypipe | |||||||||||
57 | LysoPhD | Identify Integrated Viruses | Phage | https://ieeexplore.ieee.org/document/8983280 | No code available | |||||||||||
58 | MaGplotR | CRISPR | Virus | CRISPR Screens | https://www.biorxiv.org/content/10.1101/2023.01.12.523725v1 | https://github.com/alematia/MaGplotR | ||||||||||
59 | MARVEL | Virus identification in metagenomes | Phage | random forest | https://www.frontiersin.org/articles/10.3389/fgene.2018.00304/full | https://github.com/LaboratorioBioinformatica/MARVEL | ||||||||||
60 | MetaCerberus | Genome annotation | Both | HMM-based with Ray MPP | https://doi.org/10.1093/bioinformatics/btae119 | https://github.com/raw-lab/MetaCerberus | ||||||||||
61 | metaPhage | Virus identification in metagenomes | Both | pipeline | https://mattiapandolfovr.github.io/MetaPhage/ | |||||||||||
62 | MetaPhinder | Virus identification in metagenomes | Both | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042410/ | https://github.com/vanessajurtz/MetaPhinder | |||||||||||
63 | MetaPhlAn-4.1.0 | Virus identification in metagenomes | Both | Read mapping | https://doi.org/10.1101/2024.02.19.580813 | https://github.com/biobakery/MetaPhlAn/releases/tag/4.1.0 | ||||||||||
64 | metaviralSPAdes | Genome assembly | Both | MetaviralSPAdes: assembly of viruses from metagenomic data | Bioinformatics | Oxford Academic | https://github.com/ablab/spades/tree/metaviral_publication | |||||||||||
65 | mMGE | Sequence Database | Both | mobile genetic element database | https://mai.fudan.edu.cn/mgedb/client/index.html#/ | |||||||||||
66 | mulitPHATE | Genome comparison | Phage | https://github.com/carolzhou/multiPhATE | ||||||||||||
67 | MVP | Host prediction | Both | https://academic.oup.com/nar/article/46/D1/D700/4643372?login=true | http://mvp.medgenius.info/home | |||||||||||
68 | OLGenie | Evolutionary analysis | Both | Program for estimating dN/dS in overlapping genes (OLGs); inferring purifying selection in alternative reading frames; intrahost; within-host; evolution; selection; nucleotide diversity | https://academic.oup.com/mbe/article/37/8/2440/5815567 | https://github.com/chasewnelson/OLGenie | ||||||||||
69 | palmID | RNA Virus (RdRp) search tool | Virus | Website / R | https://peerj.com/articles/14055/ | https://serratus.io/palmid | ||||||||||
70 | PB-LKS | Host prediction | Phage | k-mer profiles | https://academic.oup.com/bib/article/25/2/bbae010/7606369 | https://github.com/wanchunnie/PB-LKS | ||||||||||
71 | Phables | Viral strain reconstruction | Phage | Flow decomposition on assembly graphs | https://biorxiv.org/cgi/content/short/2023.04.04.535632v1 | https://github.com/Vini2/phables | ||||||||||
72 | PhaBox | Virus identification in metagenomes | Phage | Based on previously published tools: PhaMer, PhaTYP, PhaGCN, and CHERRY | https://arxiv.org/abs/2303.15707 | https://phage.ee.cityu.edu.hk/ | ||||||||||
73 | PHACTS | Lifestyle classification | Phage | https://pubmed.ncbi.nlm.nih.gov/22238260/ | https://github.com/deprekate/PHACTS | |||||||||||
74 | PhaGCN | Virus taxonomy | Phage | GCN | https://academic.oup.com/bioinformatics/article/37/Supplement_1/i25/6319660 | https://github.com/KennthShang/PhaGCN | ||||||||||
75 | Phage tools | Virus identification in metagenomes | Phage | https://github.com/sxh1136/Phage_tools | ||||||||||||
76 | phage_finder | Identify Integrated Viruses | Phage | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635311/ | http://phage-finder.sourceforge.net/ | |||||||||||
77 | PhageAI | Lifestyle classification | Phage | NLP, ML | https://www.biorxiv.org/content/10.1101/2020.07.11.198606v1 | https://app.phage.ai/ | ||||||||||
78 | phageboost | Identify Integrated Viruses | Phage | boost ml | https://www.biorxiv.org/content/10.1101/2020.08.09.243022v1 | http://phageboost.ml | ||||||||||
79 | PhageClouds | Genome comparison | Phage | network graphs | https://doi.org/10.1089/phage.2021.0008 | |||||||||||
80 | PhageDPO | Depolymerase finder | Phage | SVM and ANN | bit.ly/phagedpo | |||||||||||
81 | PhageHostLearn | Host prediction | Phage | https://www.nature.com/articles/s41467-024-48675-6 | https://github.com/dimiboeckaerts/PhageHostLearn | |||||||||||
82 | PhagePromoter | Promoters | Phage | artificial neural network (ANN), support vector machines (SVM) | https://academic.oup.com/bioinformatics/article/35/24/5301/5540317 | https://github.com/martaS95/PhagePromoter | ||||||||||
83 | PhageRBPdetect | Host prediction | Phage | HMMs & machine learning | https://www.mdpi.com/1999-4915/14/6/1329 | |||||||||||
84 | PhagesDB | Sequence Database | Phage | https://phagesdb.org/ | ||||||||||||
85 | PhageTB | Phage therapy | Phage | BLAST | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10076811/ | https://github.com/raghavagps/phagetb | ||||||||||
86 | PhageTerm | Predicting phage packaging mechanism | Phage | Read mapping | https://www.nature.com/articles/s41598-017-07910-5 | https://gitlab.pasteur.fr/vlegrand/ptv/-/releases | ||||||||||
87 | PhageWeb | Identify Integrated Viruses | Phage | https://www.frontiersin.org/articles/10.3389/fgene.2018.00644/full | http://computationalbiology.ufpa.br/phageweb/ | |||||||||||
88 | PHAMB | Virus identification in metagenomes | Phage | Random forest | https://www.nature.com/articles/s41467-022-28581-5 | https://github.com/RasmussenLab/phamb | ||||||||||
89 | phaMers | Virus identification in metagenomes | Phage | kmers + machine learning | https://doi.org/10.1002/adbi.201900108 | https://github.com/jondeaton/PhaMers | ||||||||||
90 | PhANNs | Genome annotation | Phage | https://journals.plos.org/ploscompbiol/article/authors?id=10.1371/journal.pcbi.1007845 | PhANNs | |||||||||||
91 | Phanotate | Phage genes | Phage | https://academic.oup.com/bioinformatics/article/35/22/4537/5480131 | https://github.com/deprekate/PHANOTATE | |||||||||||
92 | Phanta | Virus identification in metagenomes | Both | K-mer read based classification, snakemake workflow | https://www.biorxiv.org/content/10.1101/2022.08.05.502982v1.full | https://github.com/bhattlab/phanta | ||||||||||
93 | Pharokka | Genome annotation | Phage | https://doi.org/10.1093/bioinformatics/btac776 | https://github.com/gbouras13/pharokka | |||||||||||
94 | PHASTER | Identify Integrated Viruses | Phage | https://pubmed.ncbi.nlm.nih.gov/27141966/ | https://phaster.ca/ | |||||||||||
95 | PHERI | Host prediction | Phage | PHERI | https://github.com/andynet/pheri | |||||||||||
96 | PHIAF | Host prediction | Phage | GAN | https://academic.oup.com/bib/article-abstract/23/1/bbab348/6362109 | https://github.com/BioMedicalBigDataMiningLab/PHIAF | ||||||||||
97 | Phigaro | Identify Integrated Viruses | Phage | https://www.biorxiv.org/content/10.1101/598243v1 | https://github.com/bobeobibo/phigaro | |||||||||||
98 | PHISDetector | Host prediction | Phage | http://www.microbiome-bigdata.com/PHISDetector/index/ | ||||||||||||
99 | PhiSpy | Identify Integrated Viruses | Phage | PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies - PMC | https://github.com/linsalrob/PhiSpy | |||||||||||
100 | PHIST | Host prediction | Phage | k-mers | https://academic.oup.com/bioinformatics/article/38/5/1447/6460800 | https://github.com/refresh-bio/phist |