Name Category Phage, Virus, or Both Methods Citation 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

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/)

PhageDPO Depolymerase finder Phage SVM and ANN bit.ly/phagedpo 2022 Yes

Pharokka Genome annnotation Phage https://doi.org/10.1093/bioinformatics/btac776 https://github.com/gbouras13/pharokka 20230124 Yes yes

DRAMv Genome annnotation, AMG confidence scoring 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

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://github.com/ablab/spades/tree/metaviral_publication

PHAMB Genome binning Phage Random forest https://www.nature.com/articles/s41467-022-28581-5 https://github.com/RasmussenLab/phamb Yes VAMB, DeepVirFinder

vRhyme Genome binning Both Machine learning vRhyme enables binning of viral genomes from metagenomes | Nucleic Acids Research | Oxford Academic https://github.com/AnantharamanLab/vRhyme Yes No yes

mulitPHATE Genome comparison Phage https://academic.oup.com/bioinformatics/article/35/22/4537/5480131 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

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

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://github.com/soedinglab/WIsH

iPHoP Host prediction Phage https://www.biorxiv.org/content/10.1101/2022.07.28.501908v1.abstract

DeePaC Host prediction, pathogen detection 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 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, pathogen detection 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

VAPiD Human virus annotation system Virus https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2606-y https://github.com/rcs333/VAPiD No yes yes

viralintegration Identify virus integration into host genome Virus Nextflow pipeline https://github.com/nf-core/viralintegration 2023 Yes No Yes Nextflow, conda or singularity/docker Yes Yes

crassus Indetifying crassphage contigs Phage snakemake workflow https://github.com/dcarrillox/CrassUS 20220704 yes yes

BACPHLIP Lifestyle classification Phage Random Forest classifier https://pubmed.ncbi.nlm.nih.gov/33996289/ https://github.com/adamhockenberry/bacphlip 20210128 Yes Yes Yes

geNomad Mobile genetic elements Both https://github.com/apcamargo/genomad 20221015 Yes No yes

ViralMSA Multiple Sequence Alignment Virus Python script that wraps around read mappers (e.g. Minimap2) https://doi.org/10.1093/bioinformatics/btaa743 https://github.com/niemasd/ViralMSA Actively developed User needs to install at least one read mapper (ideally Minimap2) No No Yes Read mapper (ideally Minimap2) Yes Yes

PHROGs Orthologous Groups Phage https://academic.oup.com/nargab/article/3/3/lqab067/6342220

OLGenie Phage genes both inferring purifying selection in alternative reading frames https://academic.oup.com/mbe/article/37/8/2440/5815567

Phanotate Phage genes Phage https://academic.oup.com/bioinformatics/article/35/22/4537/5480131 https://github.com/deprekate/PHANOTATE

Classiphages 2.0 Phage phylogeny/taxonomy/classification Phage ANN https://www.biorxiv.org/content/10.1101/558171v1 No code available None Does not appear to be available

GraViTy Phage phylogeny/taxonomy/classification Both HMMs and genome organisation models https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0422-7 https://github.com/PAiewsakun/GRAViTy 20200224

PhaGCN Phage phylogeny/taxonomy/classification Phage GCN https://academic.oup.com/bioinformatics/article/37/Supplement_1/i25/6319660 https://github.com/KennthShang/PhaGCN

VICTOR Phage phylogeny/taxonomy/classification Phage https://academic.oup.com/bioinformatics/article/33/21/3396/3933260 https://github.com/vdclab/vdclab-wiki/blob/master/VICTOR.md

VIPtree Phage phylogeny/taxonomy/classification Phage https://academic.oup.com/bioinformatics/article/33/21/3396/3933260 https://github.com/yosuken/ViPTreeGen

VIRIDIC Phage phylogeny/taxonomy/classification Phage https://www.mdpi.com/1999-4915/12/11/1268

VIRify Phage phylogeny/taxonomy/classification Both https://www.researchgate.net/publication/362871600_VIRify_an_integrated_detection_annotation_and_taxonomic_classification_pipeline_using_virus-specific_protein_profile_hidden_Markov_models/link/6304eb9961e4553b95322c97/download https://github.com/EBI-Metagenomics/emg-viral-pipeline

VPF Class Phage phylogeny/taxonomy/classification Both https://academic.oup.com/bioinformatics/article/37/13/1805/6104829 https://github.com/biocom-uib/vpf-tools

PhageTerm Predicting phage packaging mechanism Phage Read mapping https://www.nature.com/articles/s41598-017-07910-5 https://gitlab.pasteur.fr/vlegrand/ptv/-/releases No No Yes Was written in python2, not sure if they have updated it. Not an easy tool to install

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 No No Yes

DRAD Prophage Identification Phage Dinucleotide Relative Abundance difference https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001193 Does not exist any more None

hafeZ Prophage Identification Phage Readmapping https://www.biorxiv.org/content/10.1101/2021.07.21.453177v1 https://github.com/Chrisjrt/hafeZ 20211004

LysoPhD Prophage Identification Phage https://ieeexplore.ieee.org/document/8983280 No code available None Does not appear to be available

phage_finder Prophage Identification Phage https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635311/ http://phage-finder.sourceforge.net/

phageboost Prophage Identification Phage boost ml https: