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.

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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 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 20230112

SpacePHARER CRISPR Phage CRISPR Spacer Phage-Host Pair Finder 20220906

BVBRC Cyberinfrastructure-supported virus tools Both Website Actively developed No No No website

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

DePP Depolymerase finder Phage

PhageDPO Depolymerase finder Phage SVM and ANN 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 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 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 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 20231108 No No Yes Snakemake, Python Yes Yes

MetaCerberus Genome and virome annotation Both HMM-based with Ray MPP 2023 Python Yes Yes Yes

DRAMv Genome annnotation Phage Distilling and refining annotation of metabolism 2023 Yes Yes Yes

PhANNs Genome annnotation Phage PhANNs Online only (there is a Python version that can be installed locally - contact Anca Segall, [email protected]) website (yes)

Pharokka Genome annnotation Phage 20230124 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,5

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

BacteriophageHostPrediction Host prediction Phage,5

CHERRY Host prediction Phage,5

CrisprOpenDB Host prediction Phage,5

DeepHost Host prediction Phage CNN 20220804

HostG Host prediction Phage GCN 20220316

HostPhinder Host prediction Phage k-mers 20200902

INFH-VH Host prediction Phage

MVP Host prediction Both

PHERI Host prediction Phage PHERI

PHIAF Host prediction Phage GAN

PHISDetector Host prediction Phage

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

PHP Host prediction Phage

PredPHI Host prediction Phage

RaFaH Host prediction Phage

vHulk Host prediction Phage,5

VIDHOP Host prediction Both Deep learning 20230507 Yes No Yes

VirHostMatcher Host prediction Phage oligonucleotide frequency based distance and dissimilarity measures

VirHostMatcher-Net Host prediction Virus,5

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

Virus Host DB Host prediction Both

Virus Host Predict Host prediction Both

WIsH Host prediction Phage,3%20kbp%2Dlong%20phage%20contigs.,5

DeePaC Host prediction Both CNN, ResNet, Shapley values (interpretability),,,5 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 20210123 DeePaC plugin for real-time analysis (during Illumina sequencing) Yes Yes Yes DeePaC, HiLive Yes (GPU recommended) Yes

iPHoP Host prediction Phage

DRAD Identify Integrated Viruses Phage Dinucleotide Relative Abundance difference Does not exist any more None


Viral Bioinformatics Tools
Tags Biology, Data, List
Type Google Sheet
Published 23/04/2024, 19:36:39

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