Viral Bioinformatics Tools

Need a #virus or #phage bioinformatics tool? Have a #virus or #phage bioinformatics tool? Check out this sheet and add your new tools.

  1. Home
  2. Google Sheet
  3. Viral Bioinformatics Tools

Viral Bioinformatics Tools

Need a #virus or #phage bioinformatics tool? Have a #virus or #phage bioinformatics tool? Check out this sheet and add your new tools.

biology, data, list

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 20230112

SpacePHARER CRISPR Phage CRISPR Spacer Phage-Host Pair Finder 20220906

iVirus 2.0 Cyberinfrastructure-supported virus tools Phage integrating iVirus apps on CyVerse and KBase CyVerse (, KBase (

PhageDPO Depolymerase finder Phage SVM and ANN 2022 Yes

Pharokka Genome annnotation Phage 20230124 Yes yes

DRAMv Genome annnotation, AMG confidence scoring Phage Distilling and refining annotation of metabolism 2023 Yes Yes Yes

coronaSPAdes Genome assembly Both HMM-synteny guided assembly (works for all viruses)

metaviralSPAdes Genome assembly Both MetaviralSPAdes: assembly of viruses from metagenomic data | Bioinformatics | Oxford Academic

PHAMB Genome binning Phage Random forest Yes VAMB, DeepVirFinder

vRhyme Genome binning Both Machine learning vRhyme enables binning of viral genomes from metagenomes | Nucleic Acids Research | Oxford Academic Yes No yes

mulitPHATE Genome comparison Phage

PhageClouds Genome comparison Phage network graphs I think this is a website, but its down. Cant find the source code

CheckV Genome completeness Both 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

viralVerify Genome completeness Both

DeepHost Host prediction Phage CNN 20220804

HostG Host prediction Phage GCN 20220316

HostPhinder Host prediction Phage k-mers 20200902

PHIAF Host prediction Phage GAN

PHIST Host prediction Phage k-mers No No Yes Yes Yes

RaFaH Host prediction Phage

VIDHOP Host prediction Both Deep learning Yes No Yes

VirHostMatcher Host prediction Phage oligonucleotide frequency based distance and dissimilarity measures

VirMatcher Host prediction Phage Leveraging multiple methods and assigning a confidence score 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,3%20kbp%2Dlong%20phage%20contigs.

iPHoP Host prediction Phage

DeePaC Host prediction, pathogen detection Both CNN, ResNet, Shapley values (interpretability),, 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 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 No yes yes

viralintegration Identify virus integration into host genome Virus Nextflow pipeline 2023 Yes No Yes Nextflow, conda or singularity/docker Yes Yes

crassus Indetifying crassphage contigs Phage snakemake workflow 20220704 yes yes

BACPHLIP Lifestyle classification Phage Random Forest classifier 20210128 Yes Yes Yes

geNomad Mobile genetic elements Both 20221015 Yes No yes

ViralMSA Multiple Sequence Alignment Virus Python script that wraps around read mappers (e.g. Minimap2) 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

OLGenie Phage genes both inferring purifying selection in alternative reading frames

Phanotate Phage genes Phage

Classiphages 2.0 Phage phylogeny/taxonomy/classification Phage ANN No code available None Does not appear to be available

GraViTy Phage phylogeny/taxonomy/classification Both HMMs and genome organisation models 20200224

PhaGCN Phage phylogeny/taxonomy/classification Phage GCN

VICTOR Phage phylogeny/taxonomy/classification Phage

VIPtree Phage phylogeny/taxonomy/classification Phage

VIRIDIC Phage phylogeny/taxonomy/classification Phage

VIRify Phage phylogeny/taxonomy/classification Both

VPF Class Phage phylogeny/taxonomy/classification Both

PhageTerm Predicting phage packaging mechanism Phage Read mapping 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) No No Yes

DRAD Prophage Identification Phage Dinucleotide Relative Abundance difference Does not exist any more None

hafeZ Prophage Identification Phage Readmapping 20211004

LysoPhD Prophage Identification Phage No code available None Does not appear to be available

phage_finder Prophage Identification Phage

phageboost Prophage Identification Phage boost ml https:

Viral Bioinformatics Tools
Tags Biology, Data, List
Type Google Sheet
Published 17/03/2023, 16:07:23