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 https://github.com/soedinglab/spacepharer 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

OLGenie Diversity and selection 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 20221202 Perl No No Yes Perl Yes Yes

SNPGenie Diversity and selection analysis Both Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data; intrahost; within-host; evolution; selection; nucleotide diversity https://academic.oup.com/bioinformatics/article/31/22/3709/241742 https://github.com/chasewnelson/snpgenie 20230822 Perl Yes No Yes Perl Yes Yes

VCFgenie Diversity and selection analysis Both Program for reproducibly filtering VCF files and eliminating false positive variants; intrahost; within-host; evolution; selection; nucleotide diversity In revision https://github.com/chasewnelson/VCFgenie 20220825 Python No No Yes Python libraries argparse, collections, numpy, operator, os, re, scipy, sys, typing, vcf, (pyvcf) Yes 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://doi.org/10.1093/bioinformatics/btae119 https://github.com/raw-lab/MetaCerberus 2023 Python Yes Yes Yes

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/

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

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

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

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

INFH-VH Host prediction Phage https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3082-0 https://github.com/liudan111/ILMF-VH

MVP Host prediction Both https://academic.oup.com/nar/article/46/D1/D700/4643372?login=true http://mvp.medgenius.info/home

PHERI Host prediction Phage PHERI https://github.com/andynet/pheri

PHIAF Host prediction Phage GAN https://academic.oup.com/bib/article-abstract/23/1/bbab348/6362109 https://github.com/BioMedicalBigDataMiningLab/PHIAF

PHISDetector Host prediction Phage http://www.microbiome-bigdata.com/PHISDetector/index/

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

PHP Host prediction Phage https://github.com/congyulu-bioinfo/PHP

PredPHI Host prediction Phage https://github.com/xialab-ahu/PredPHI

RaFaH Host prediction Phage https://www.sciencedirect.com/science/article/pii/S2666389921001008 https://sourceforge.net/projects/rafah/

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

VIDHOP Host prediction Both Deep learning https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7454304/ https://github.com/flomock/vidhop 20230507 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

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

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/

Virus Host Predict Host prediction Both https://github.com/youngfran/virus_host_predict

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

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