Name Category Individual, multiple, or virome Phage, Virus, or Both Methods Citation Google Scholar Link to Cluster Representing the Paper URL Last update (YYYMMDD) Notes Install from conda Install from pip Install from source Database size if required for download Dependencies Runs on a laptop Runs on a cluster @
MaGplotR CRISPR Virus CRISPR Screens https://www.biorxiv.org/content/10.1101/2023.01.12.523725v1 https://github.com/alematia/MaGplotR 20230112
SpacePHARER CRISPR Phage CRISPR Spacer Phage-Host Pair Finder https://www.biorxiv.org/content/10.1101/2020.05.15.090266v1 spacepharer.soedinglab.org 20220906
BVBRC Cyberinfrastructure-supported virus tools Both Website http://bvbrc.org https://bitbucket.org/srouxjgi/iphop Actively developed No No No website
iVirus 2.0 Cyberinfrastructure-supported 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/)
DePP Depolymerase finder Phage https://timskvortsov.github.io/WebDePP/
PhageDPO Depolymerase finder Phage SVM and ANN bit.ly/phagedpo 2022 Yes
VIPERA Evolutionary analysis Virus Phylogenetic and population genetics-based analysis of intra-patient SARS-CoV-2 https://doi.org/10.1101/2023.10.24.561010 https://scholar.google.es/scholar?oi=bibs&hl=en&cluster=7842293868566810584 https://github.com/PathoGenOmics-Lab/VIPERA 20231108 No No Yes Snakemake, Python Yes Yes
MetaCerberus Genome and virome annotation Both HMM-based with Ray MPP https://www.biorxiv.org/content/10.1101/2023.08.10.552700v1 https://github.com/raw-lab/MetaCerberus 2023
DRAMv Genome annnotation Phage Distilling and refining annotation of metabolism https://academic.oup.com/nar/article/48/16/8883/5884738 https://github.com/WrightonLabCSU/DRAM 2023 Yes Yes Yes
PhANNs Genome annnotation Phage https://journals.plos.org/ploscompbiol/article/authors?id=10.1371/journal.pcbi.1007845 PhANNs Online only (there is a Python version that can be installed locally - contact Anca Segall, [email protected]) website (yes)
Pharokka Genome annnotation Phage https://doi.org/10.1093/bioinformatics/btac776 https://github.com/gbouras13/pharokka 20230124 Yes yes
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
metaviralSPAdes Genome assembly Both MetaviralSPAdes: assembly of viruses from metagenomic data | Bioinformatics | Oxford Academic https://scholar.google.com/scholar?cluster=3947397301410156503&hl=en&as_sdt=0,5 https://github.com/ablab/spades/tree/metaviral_publication
mulitPHATE Genome comparison Phage https://github.com/carolzhou/multiPhATE
PhageClouds Genome comparison Phage network graphs https://doi.org/10.1089/phage.2021.0008 I think this is a website, but its down. Cant find the source code
CheckV Genome completeness Both https://www.biorxiv.org/content/10.1101/2020.05.06.081778v1 https://bitbucket.org/berkeleylab/checkv/src/master/ 20220906 Not recommended for prophages: from the FAQ: Q: Can I use CheckV to predict (pro)viruses from whole (meta)genomes? A: Possibly, though this has not been tested. X x
viralComplete Genome completeness Both https://github.com/ablab/viralComplete/
viralVerify Genome completeness Both https://github.com/ablab/viralVerify/
DeepHost Host prediction Phage CNN https://academic.oup.com/bib/article-abstract/23/1/bbab385/6374063?redirectedFrom=fulltext https://github.com/deepomicslab/DeepHost 20220804
HostG Host prediction Phage GCN https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01180-4 https://github.com/KennthShang/HostG 20220316
HostPhinder Host prediction Phage k-mers https://pubmed.ncbi.nlm.nih.gov/27153081/ https://github.com/julvi/HostPhinder 20200902
MVP Host prediction Both https://academic.oup.com/nar/article/46/D1/D700/4643372?login=true http://mvp.medgenius.info/home
PHIAF Host prediction Phage GAN https://academic.oup.com/bib/article-abstract/23/1/bbab348/6362109 https://github.com/BioMedicalBigDataMiningLab/PHIAF
PHIST Host prediction Phage k-mers https://academic.oup.com/bioinformatics/article/38/5/1447/6460800 https://github.com/refresh-bio/phist No No Yes Yes Yes
RaFaH Host prediction Phage https://www.sciencedirect.com/science/article/pii/S2666389921001008 https://sourceforge.net/projects/rafah/
VIDHOP Host prediction Both Deep learning https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454304/ https://github.com/flomock/vidhop Yes No Yes
VirHostMatcher Host prediction Phage oligonucleotide frequency based distance and dissimilarity measures https://pubmed.ncbi.nlm.nih.gov/27899557/ https://github.com/jessieren/VirHostMatcher
VirMatcher Host prediction Phage Leveraging multiple methods and assigning a confidence score https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(20)30456-X https://bitbucket.org/MAVERICLab/virmatcher/src/master/ 20220429 Leveraging multiple methods (host CRISPR-spacers, integrated prophage, host tRNA genes, and k-mer signatures calculated by WIsH) Yes NCBI BLAST, tRNA-Scan SE, MINCED, WIsH Maybe (linux system) Yes
Virus Host DB Host prediction Both https://pubmed.ncbi.nlm.nih.gov/26938550/ https://www.genome.jp/virushostdb/
WIsH Host prediction Phage https://academic.oup.com/bioinformatics/article/33/19/3113/3964377#:~:text=WIsH%20predicts%20prokaryotic%20hosts%20of,3%20kbp%2Dlong%20phage%20contigs. https://scholar.google.com/scholar?cluster=10819291780843937718&hl=en&as_sdt=0,5 https://github.com/soedinglab/WIsH
PHERI Host prediction Phage PHERI https://github.com/andynet/pheri
PHP Host prediction Phage https://github.com/congyulu-bioinfo/PHP
BacteriophageHostPrediction Host prediction Phage https://www.nature.com/articles/s41598-021-81063-4 https://scholar.google.com/scholar?cluster=3449135478742512651&hl=en&as_sdt=0,5 https://github.com/dimiboeckaerts/BacteriophageHostPrediction
CrisprOpenDB Host prediction Phage https://doi.org/10.1093/nar/gkab133 https://scholar.google.com/scholar?cluster=17629824852368187775&hl=en&as_sdt=0,5 https://github.com/edzuf/CrisprOpenDB
vHulk Host prediction Phage https://www.biorxiv.org/content/10.1101/2020.12.06.413476v1 https://scholar.google.com/scholar?cluster=11368629964070696550&hl=en&as_sdt=0,5
Virus Host Predict Host prediction Both https://github.com/youngfran/virus_host_predict
INFH-VH Host prediction Phage https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3082-0 https://github.com/liudan111/ILMF-VH
CHERRY Host prediction Phage https://academic.oup.com/bib/article/23/5/bbac182/6589865 https://scholar.google.com/scholar?cluster=2950777594899421181&hl=en&as_sdt=0,5 https://github.com/KennthShang/CHERRY
PHISDetector Host prediction Phage http://www.microbiome-bigdata.com/PHISDetector/index/
VirHostMatcher-Net Host prediction Virus https://academic.oup.com/nargab/article/2/2/lqaa044/5861484?login=true https://scholar.google.com/scholar?cluster=11117917300880093415&hl=en&as_sdt=0,5 https://github.com/WeiliWw/VirHostMatcher-Net
PredPHI Host prediction Phage https://github.com/xialab-ahu/PredPHI
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://scholar.google.com/scholar?cluster=15260546894544767325&hl=en&as_sdt=0,5 https://gitlab.com/dacs-hpi/deepac 20221216 Detection of novel human pathogens from raw short/long reads, contigs, genomes; interpretability toolkit available Yes Yes Yes Tensorflow, shap Yes (GPU recommended) Yes
DeePaC-Live Host prediction Both ResNet https://academic.oup.com/bib/article/22/6/bbab269/6326527 https://gitlab.com/dacs-hpi/deepac-live 20210123 DeePaC plugin for real-time analysis (during Illumina sequencing) Yes Yes Yes DeePaC, HiLive Yes (GPU recommended) Yes
iPHoP Host prediction Phage https://www.biorxiv.org/content/10.1101/2022.07.28.501908v1.abstract
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 None
geNomad Identify Integrated Viruses Both https://github.com/apcamargo/genomad 20221015 Yes No yes
hafeZ Identify Integrated Viruses Phage Readmapping https://www.biorxiv.org/content/10.1101/2021.07.21.453177v1 https://github.com/Chrisjrt/hafeZ 20211004
LysoPhD Identify Integrated Viruses Phage https://ieeexplore.ieee.org/document/8983280 No code available None Does not appear to be available
phage_finder Identify Integrated Viruses Phage https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635311/ http://phage-finder.sourceforge.net/
phageboost Identify Integrated Viruses Phage boost ml https://www.biorxiv.org/content/10.1101/2020.08.09.243022v1 http://phageboost.ml
PhageWeb Identify Integrated Viruses Phage https://www.frontiersin.org/articles/10.3389/fgene.2018.00644/full http://computationalbiology.ufpa.br/phageweb/ There is an API but it submits jobs to their server!
PHASTER Identify Integrated Viruses Phage https://pubmed.ncbi.nlm.nih.gov/27141966/ https://phaster.ca/ Not available for download. Did not run all genomes on their webserver as they are having issues (Ma