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awesome-virome

A listing of software, tools and databases useful for virome analysis
https://github.com/shandley/awesome-virome

Last synced: 1 day ago
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  • Interactive Dashboard

    • Launch Dashboard - virome/citations.html) | [Explore Publication Impact](https://shandley.github.io/awesome-virome/publication_impact.html) | [Compare Tools](https://shandley.github.io/awesome-virome/comparison.html)

  • Tool Selection Guide

  • Virus and Phage Identification

    • Metagenome Analysis

      • HoloVir - Pipeline for taxonomic classification and gene function assignment. [Perl]
      • VIBRANT - Virus identification by combining boundary detection with annotation. [Python]
      • Cenote-Taker 3 - Hallmark gene discovery, gene annotation, flanking host gene removal. [Linux/MacOS] [conda] [v0.1.0, 2023]
      • Cenote-Taker 2 - Scans contigs for virus hallmark genes, removes flanking host DNA from prophages, makes annotated genome maps. [conda, pip] [v2.1.5, 2022]
      • CoCoNet - Neural networks for viral contig identification. [pip] [Python]
      • crassus - Snakemake workflow for phage discovery. [conda] [Python]
      • Deep6 - Machine learning based virus identification. [Python]
      • DeepVirFinder - Neural network approach for viral contig identification. [Python]
      • FastViromeExplorer - Detects viral sequences and predicts abundance by pseudoalignment of reads to a database. [Java]
      • hecatomb - Pipeline for virus identification from metagenomic data. [Nextflow]
      • HoloVir - Pipeline for taxonomic classification and gene function assignment. [Perl]
      • Cenote-Taker 3 - Hallmark gene discovery, gene annotation, flanking host gene removal. [Linux/MacOS] [conda] [v0.1.0, 2023]
      • crassus - Snakemake workflow for phage discovery. [conda] [Python]
      • Cenote-Taker 2 - Scans contigs for virus hallmark genes, removes flanking host DNA from prophages, makes annotated genome maps. [conda, pip] [v2.1.5, 2022]
      • CoCoNet - Neural networks for viral contig identification. [pip] [Python]
      • Deep6 - Machine learning based virus identification. [Python]
      • DePhT - Deep-learning Phage Taxonomy for phage identification. [conda] [Python]
      • FastViromeExplorer - Detects viral sequences and predicts abundance by pseudoalignment of reads to a database. [Java]
      • GenomePeek - Taxonomic classification of multiple domains. [Python]
      • hecatomb - Pipeline for virus identification from metagenomic data. [Nextflow]
      • HoloVir - Pipeline for taxonomic classification and gene function assignment. [Perl]
      • INHERIT - BERT embedding-based phage identification. [Python]
      • INSaFLU-TELEVIR - Platform for virus identification and characterization. [Python]
      • isling - Split read alignment for virus identification. [Python]
      • Jaeger - Phage identification in metagenomes. [Python]
      • Jovian - Public health toolkit focused on human viruses. [Nextflow]
      • LazyPipe - Taxonomic profiling and reference-based detection. [Nextflow]
      • MARVEL - Random forest classifier for phage identification (not for prophages). [Python]
      • metaPhage - Pipeline for phage and virus identification. [conda] [Nextflow]
      • MetaPhinder - Integrates BLAST hits to multiple phage genomes to identify phage sequences. [Python]
      • MetaPhlAn 4.1.0 - Read mapping-based virus identification. [conda, pip] [Python]
      • PhaBox - Integrates several phage tools: PhaMer, PhaTYP, PhaGCN, and CHERRY. [conda] [Python]
      • Phage tools - Collection of tools for predicting and identifying phage in metagenomes. [Python]
      • INHERIT - BERT embedding-based phage identification. [Python]
      • isling - Split read alignment for virus identification. [Python]
      • Jaeger - Phage identification in metagenomes. [Python]
      • Jovian - Public health toolkit focused on human viruses. [Nextflow]
      • MetaPhinder - Integrates BLAST hits to multiple phage genomes to identify phage sequences. [Python]
      • LazyPipe - Taxonomic profiling and reference-based detection. [Nextflow]
      • MARVEL - Random forest classifier for phage identification (not for prophages). [Python]
      • metaPhage - Pipeline for phage and virus identification. [conda] [Nextflow]
      • virAnnot - Pipeline for OTU assignment in viral sequences. [source] [Python]
      • VirFinder - Neural network and machine learning for virus identification. [R]
      • Virhunter - Deep learning approach for virus identification. [Python]
      • PHAMB - Random forest based phage identification. [conda] [Python]
      • MetaPhlAn 4.1.0 - Read mapping-based virus identification. [conda, pip] [Python]
      • PhaBox - Integrates several phage tools: PhaMer, PhaTYP, PhaGCN, and CHERRY. [conda] [Python]
      • Phage tools - Collection of tools for predicting and identifying phage in metagenomes. [Python]
      • PHAMB - Random forest based phage identification. [conda] [Python]
      • phaMers - K-mer and machine learning phage identification. [Python]
      • phaMers - K-mer and machine learning phage identification. [Python]
      • Phanta - K-mer read based classification via snakemake workflow. [yaml] [Python]
      • Phanta - K-mer read based classification via snakemake workflow. [yaml] [Python]
      • Seeker - LSTM-based phage identification (not recommended for prophages). [pip] [Python]
      • PIGv - Giant virus identification using Metabat binning, k-mer scoring, and marker genes. [source] [Python]
      • PPR-Meta - Convolutional neural network for phage prediction. [Python]
      • Prophage Tracer - Split read alignment for prophage identification. [Python]
      • VFM - Virus finder in metagenomic data. [Python]
      • Seeker - LSTM-based phage identification (not recommended for prophages). [pip] [Python]
      • Serratus - Website for virus discovery from public sequencing data. [cloud platform]
      • VIGA - Viral genome assembler. [pip] [Python]
      • VIP - Integrated pipeline for virus identification. [Python]
      • ViralCC - Viral sequence identification via machine learning. [Python]
      • VIP - Integrated pipeline for virus identification. [Python]
      • ViralCC - Viral sequence identification via machine learning. [Python]
      • Serratus - Website for virus discovery from public sequencing data. [cloud platform]
      • ViralConsensus - Viral consensus sequence calling from sequencing data. [source] [Python]
      • VFM - Virus finder in metagenomic data. [Python]
      • VIBRANT - Virus identification by combining boundary detection with annotation. [Python]
      • VIGA - Viral genome assembler. [pip] [Python]
      • ViralConsensus - Viral consensus sequence calling from sequencing data. [source] [Python]
      • viralMetagenomicsPipeline - Snakemake workflow combining virSorter and VirFinder. [Python]
      • ViralWasm - WebAssembly tools for virus identification in the browser. [JavaScript]
      • viralMetagenomicsPipeline - Snakemake workflow combining virSorter and VirFinder. [Python]
      • ViralWasm - WebAssembly tools for virus identification in the browser. [JavaScript]
      • VirFinder - Neural network and machine learning for virus identification. [R]
      • Virhunter - Deep learning approach for virus identification. [Python]
      • virMiner - Random forest approach for virus identification. [R]
      • VirNet - Neural network for phage identification. [Python]
      • ViroProfiler - Comprehensive phage profiling pipeline. [Nextflow]
      • viraMiner - CNN classifier for virus identification. [Python]
      • virAnnot - Pipeline for OTU assignment in viral sequences. [source] [Python]
      • VirSorter2 - Random forest classifier for virus detection. [conda] [Python] [v2.2.4, 2023]
      • Virtifier - LSTM neural network for virus identification. [Python]
      • Virtus - Virus sequence detection workflow. [Snakemake]
      • virus_prediction - Nextflow pipeline with virSorter. [Nextflow]
      • ViruSpy - Virus detection pipeline. [Python]
      • VirMine - Pipeline for virus identification. [Perl]
      • virMiner - Random forest approach for virus identification. [R]
      • VirNet - Neural network for phage identification. [Python]
      • ViroProfiler - Comprehensive phage profiling pipeline. [Nextflow]
      • VirSorter - Detection of viral sequences from microbial genomic data. [bioconda] [Perl] [legacy]
      • VirSorter2 - Random forest classifier for virus detection. [conda] [Python] [v2.2.4, 2023]
      • Virtifier - LSTM neural network for virus identification. [Python]
      • Virtus - Virus sequence detection workflow. [Snakemake]
      • virus_prediction - Nextflow pipeline with virSorter. [Nextflow]
      • ViruSpy - Virus detection pipeline. [Python]
      • VirusSeeker - Pipeline for virus detection from sequence data. [source] [Perl]
      • vRhyme - Machine learning for viral binning from metagenomes. [conda] [Python]
      • What_the_phage - Nextflow workflow combining multiple phage identification tools. [Nextflow]
      • VirusSeeker - Pipeline for virus detection from sequence data. [source] [Perl]
      • vRhyme - Machine learning for viral binning from metagenomes. [conda] [Python]
      • What_the_phage - Nextflow workflow combining multiple phage identification tools. [Nextflow]

    • Integrated Viruses

      • hafeZ - Readmapping approach for integrated phage identification. [Python]
      • LysoPhD - Phage identification tool (code not available).
      • phage_finder - Pipeline for prophage identification. [Perl] [legacy]
      • phageboost - Machine learning with boost algorithm for prophage detection. [R]
      • PhageWeb - Web server for phage identification (API available). [web service]
      • DRAD - Dinucleotide Relative Abundance difference method (no longer available).
      • PHASTER - Rapid identification and annotation of prophage sequences (web service only). [web service]
      • Phigaro - Prophage prediction tool. (Note: downloads uncompressed file from Russian server). [Python]
      • DRAD - Dinucleotide Relative Abundance difference method (no longer available).
      • hafeZ - Readmapping approach for integrated phage identification. [Python]
      • LysoPhD - Phage identification tool (code not available).
      • Prophet - Prophage prediction tool. (Note: requires unsupported legacy software). [Perl] [legacy]
      • Prophinder - Web-based prophage detection tool. [web service]
      • VAPiD - Virus genome annotation and identification tool. [pip] [Python]
      • viralintegration - Nextflow pipeline for detecting viral integration sites. [conda] [Nextflow]
      • geNomad - Tool for identifying viral sequences, including proviruses. [conda] [Python] [v1.6.0, 2023]
      • geNomad - Tool for identifying viral sequences, including proviruses. [conda] [Python] [v1.6.0, 2023]

    • RNA Virus Identification

      • RdRp-scan - Search against the RdRp database. [source] [Python]
      • rdrpsearch - Iterative HMM search of viral RdRp to detect distant homologs. [source] [Python]
      • RNA-Virus-Flow - Pipeline for RNA virus assembly and analysis. [Nextflow]
      • palmID - RNA virus RdRp search tool with R interface. [source, R] [R]

  • Tool Comparison Matrix

  • Acknowledgments

  • Top Packages by Category

  • Host Prediction

    • RNA Virus Identification

      • BacteriophageHostPrediction - Computational methods for phage-host prediction. [Python]
      • CrisprOpenDB - CRISPR spacer database for phage-host prediction. [Python]
      • DeePaC - CNN, ResNet for detection of novel human pathogens. [conda, pip] [Python]
      • DeePaC-Live - DeePaC plugin for real-time analysis during sequencing. [conda, pip] [Python]
      • HostG - Graph convolutional network for phage host prediction. [Python] [v1.0, 2022]
      • HostPhinder - K-mer based phage host prediction. [Python]
      • INFH-VH - Integrating different features for virus-host prediction. [Python]
      • iPHoP - Integrated approach for phage host prediction (formerly iPHoP). Documentation at [iphop.readthedocs.io](https://iphop.readthedocs.io/). [Python] [v1.1.0, 2023]
      • MVP - Microbe-virus database with prediction tools. [web service]
      • PB-LKS - K-mer profiles for phage-bacteria prediction. [Python]
      • PhageHostLearn - Machine learning for phage-host prediction. [Python]
      • PhageRBPdetect - HMMs & machine learning for receptor-binding protein detection. [Python]
      • PHISDetector - Phage-host interaction detection. [web service]
      • PHIST - K-mer based phage-host prediction. [source] [C++]
      • PHP - Phage host prediction tool. [Python]
      • PHERI - Phage-host interaction prediction tool. [Python]
      • PHIAF - GAN-based phage-host interaction prediction. [Python]
      • PHPGCA - Similarity graphs for phage-host prediction. [Python]
      • PredPHI - Phage-host interaction prediction. [Python]
      • RaFaH - Random Forest approach for phage host prediction. [Python]
      • vHulk - Virus host prediction tool. [Python]
      • VIDHOP - Deep learning for virus-host prediction. [conda] [Python]
      • VirHostMatcher - Oligonucleotide frequency-based host prediction. [Python]
      • VirHostMatcher-Net - Network-based virus-host prediction. [Python]
      • VirMatcher - Multiple methods for phage host prediction with confidence scores. [conda] [Python] [v1.0, 2022]
      • Virus Host DB - Database for virus-host relationships. [web service]
      • Virus Host Predict - Host prediction for viral sequences. [Python]
      • WIsH - Phage-host prediction using genome homology. [C++]

  • Genome Analysis

    • Genome Annotation

      • DRAMv - Distilling and refining annotation of metabolism for phages. [conda, pip] [Python] [v1.4.6, 2023]
      • MetaCerberus - HMM-based annotation with Ray MPP. [conda, pip] [Python]
      • PhANNs - Phage annotation neural networks. (Python version available via contact) [Python]

    • Genome Assembly

      • metaviralSPAdes - Assembler for viruses from metagenomic data. [C++]
      • VEGA - Snakemake workflow for viral genome assembly. [conda] [Snakemake]

    • Genome Completeness

      • CheckV - Quality assessment for viral genomes. (Not recommended for prophages) [conda, pip] [Python] [v1.0.1, 2022]
      • viralComplete - Tool for checking viral genome completeness. [Python]
      • viralVerify - Verification of viral contigs. [Python]

    • Genome Comparison

      • mulitPHATE - Multi-phage annotation and comparison tool. [Python]
      • PhageClouds - Network graphs for phage comparison (website down, source code not found).

    • Gene Finding

      • PhiSpy - While primarily for prophage identification, includes ORF prediction capabilities. [conda, pip] [Python]
      • GLIMMER - Gene finder originally designed for bacteria but frequently used for phage genomes. [source] [C++]
      • VIGOR - Viral genome annotation tool designed specifically for viral genomes, primarily eukaryotic viruses. [source] [Java/Perl]
      • PhageTerm - Tool for identifying phage termini and packaging mechanisms, helpful for ORF identification. [source] [Python]
      • GeneMarkS - Gene prediction tool with specific models for viral sequences. [web service] [Perl/C++]
      • GeneMarkS-2 - Improved version of GeneMarkS with enhanced performance for phage genomes. [web service] [Perl/C++]
      • PhageBoost - Machine learning tool for identifying structural proteins in phage genomes. [R]
      • VGAS - Comprehensive pipeline for viral genome annotation including gene finding. [source] [Python]

  • Taxonomy

    • Gene Finding

      • BERTax - BERT-based viral taxonomy tool. [Python]
      • Classiphages 2.0 - Artificial neural network for phage classification (code not available).
      • GraViTy - HMMs and genome organization models for virus taxonomy. [R]
      • VIPtree - Viral proteomic tree generation tool. [Perl]
      • VIRIDIC - Virus intergenomic distance calculator. [R]
      • VIRify - Nextflow pipeline for viral taxonomy. [Nextflow]
      • VirusTaxo - K-mer enrichment method for viral taxonomy. [source] [Python]
      • VPF Tools - Viral protein family analysis tools. [Python]
      • PhaGCN - Graph convolutional network for phage taxonomy. [Python] [v1.0, 2022]
      • vConTACT - Whole-genome gene-sharing networks for virus taxonomy. [Python] [legacy]
      • vConTACT2.0 - Updated version of vConTACT with improved performance. [Python] [v0.9.19, 2023]
      • VICTOR - Genome-based phylogeny and classification of phages. [web service]

  • Databases

    • Gene Finding

      • FDA ARGOS - Curated database of reference genomes of microbial sequences, for diagnostic use. [web service] [Updated 2023]
      • ICTV Virus Metadata Resource (VMR) - Curated database of sequences of exemplars for each classified virus species. [Updated 2023]
      • NCBI RefSeq - Curated database of annotated genomic, transcript, and protein sequence records: viruses (ca. 8500 complete viral genomes), prokaryotes, eukaryotes. [Updated 2023]
      • NCBI GenBank - Uncurated database of all publicly available nucleotide sequences, annotated. [Updated 2023]
      • Reference Viral DataBase (RVDB), nucleic version - Curated database of virus nucleotide sequences, available as Unclustered (U-) and Clustered (C-) nucleotide sequence files. [Updated 2023]
      • Reference Viral DataBase (RVDB), protein version - Protein version (RVDB-prot and RVDB-prot-HMM) of the curated U-RVDB described above. [Updated 2023]
      • SIB Viral reference sequences - Curated database of annotated viral genomes generated by the Swiss Institute of Bioinformatics (SIB). [Updated 2023]
      • UniProt Virus proteomes - Curated and annotated database of proteomic virus references (ca. 10,000 virus reference proteomes). [Updated 2023]
      • VirMet - In-house database download from GenBank of viral references. [Python]
      • Virosaurus - Curated database of virus sequences for clinical metagenomics, clustered (non-redundant). [Updated 2022]
      • Virion - An open database of vertebrate-virus interactions. [R]

  • Sequence Databases

    • Gene Finding

      • CHVD - Comprehensive human virus database. [2021]
      • Earth Virome - Collection of viral sequences from environmental samples. [2021]
      • GOV-RNA - Global Ocean RNA viruses sequence database. [2021]
      • GOV2.0 - Global Ocean DNA viruses sequence database. [2021]
      • GPDB - Gut phage database. [2021]
      • GVD - Global virome database. [2020]
      • KEGG Virus - KEGG collection of virus genomes. [Updated 2023]
      • mMGE - Mobile genetic element database. [Updated 2023]
      • PhagesDB - Database of phage genomes. [Updated 2023]
      • ViromeDB - Public collection of >162,000 viral sequences. [2019]
      • Viruses.String - Virus-host protein-protein interactions database. [Updated 2022]

  • Functional Analysis

    • Evolutionary Analysis

      • OLGenie - Program for estimating dN/dS in overlapping genes. [source, Perl] [Perl]
      • SNPGenie - Program for estimating πN/πS and diversity measures. [conda, Perl] [Perl]
      • VCFgenie - Program for filtering VCF files and eliminating false positive variants. [source, Python] [Python]
      • VIPERA - Phylogenetic and population genetics analysis of intra-patient SARS-CoV-2. [source] [R]

    • Lifestyle Classification

      • PhageAI - NLP, ML for phage lifestyle classification. [pip] [Python]
      • BACPHLIP - Random Forest classifier for phage lifestyle. [conda, pip] [Python] [v0.9.6, 2023]
      • PHACTS - Phage classification tool suite. [Python]

    • Phage-specific Analysis

      • PHROGs - Phage-specific orthologous groups. [Database, 2021]
      • PHRED - Phage receptor identification tool (no longer available).
      • SpikeHunter - Phage tail spike identification using protein embeddings. [Python]

    • Viral Orthologous Groups

      • efam - Expanded metaproteome-supported HMM profile database of viral protein families. [2020]
      • pVOGs - Prokaryotic virus orthologous groups. [Database]
      • VogDB - Virus orthologous groups database. [Database, Updated 2023]

  • CRISPR Analysis

    • Viral Orthologous Groups

      • MaGplotR - CRISPR screen visualization tool. [R]
      • SpacePHARER - CRISPR spacer phage-host pair finder. [C++]

  • Sequence Analysis

    • Multiple Sequence Alignment

      • ViralMSA - Python script for viral multiple sequence alignment using read mappers. [source] [Python]

    • Sequence Translation

      • pygenetic_code - C and Python tools for genetic code translation. [conda, pip] [Python]

  • Visualization and Infrastructure

    • Cyberinfrastructure

      • BVBRC - BV-BRC website for virus bioinformatics. [web service]
      • iVirus 2.0 - Integrated iVirus apps on CyVerse and KBase. [web service]

    • Plaque Analysis

  • Other Tools

    • Simulation

      • FAVITES - Simulate contact networks, transmission, phylogenies, and sequences. [source] [Python]
      • FAVITES-Lite - Lighter version of FAVITES. [source] [Python]

    • Quality Control

      • ViromeQC - Virome quality control and contamination assessment. [source] [Python]

    • Amplicon Analysis

      • vAMPirus - Nextflow pipeline for virus amplicon processing and analysis. [conda] [Nextflow]

    • Viral Strain Reconstruction

      • COBRA - Viral strain reconstruction using contig overlaps. [Python]
      • Phables - Flow decomposition on assembly graphs for phage strain reconstruction. [conda, pip] [Python]
      • VStrains - Viral strain reconstruction from metagenomic data. [Python]

    • Transduction

      • TrIdent - Transduction identification via read coverage pattern matching. [R]

    • Interaction Analysis

      • DeepVHPPI - Deep learning for virus-host protein-protein interactions. [Python]
      • DePP - Depolymerase finder for phages. [web service]
      • PhageDPO - SVM and ANN for phage depolymerase prediction. [Python]
      • PhageTB - BLAST-based phage therapy tools. [Python]
      • PhageTerm - Predicting phage packaging mechanism. [source] [Python]
      • PhagePromoter - ANN, SVM for phage promoter prediction. [source] [Python]
      • VIRMOTIF - Tool for identifying viral genome motifs. [Python]

    • Antimicrobial Resistance Analysis

      • AMRFinder - NCBI's tool for identifying resistance genes, can be applied to phage genomes. [C++]
      • PHANOTATE-AMR - Extension adding AMR gene identification in phages. [Python]
      • ResFinder - Identifies resistance genes in bacteriophages. [Python]
      • VirAMR - Detects antimicrobial resistance genes in viral genomes. [Python]

    • Structural Analysis Tools

      • HNADOCK - Modeling of nucleic acid-protein complexes, useful for viral proteins. [web service]
      • I-TASSER - Widely used for viral protein structure prediction. [web service]
      • VIPERdb - Virus particle explorer database with structure visualization. [web service]
      • VIRALpro - Viral capsid and tail protein prediction. [web service]

    • Viral Metatranscriptomics

      • VirMine-RNA - Focused on detecting RNA viruses in transcriptomic data. [Python]
      • VirusTAP - Transcriptome Assembler Pipeline for viral sequence discovery. [Perl]

    • Viral Quasispecies Analysis

      • CliqueSNV - Reconstruction of virus haplotypes in a mixed population. [Java]
      • QuRe - Viral quasispecies reconstruction tool. [Java]
      • ShoRAH - Short reads assembly into haplotypes for viral population. [C++]
      • V-pipe - Pipeline for viral population analysis. [Nextflow]
      • ViQuaS - Viral Quasispecies reconstruction. [Python]

    • Cloud-based Viral Analysis

      • CloVR-Microbe - Cloud-based viral metagenomics pipeline. [Perl]
      • Viral Beacon - Cloud platform for virus sequence sharing and analysis. [Python]
      • Viral-NGS - Broad Institute's viral genomic analysis on cloud. [Python]

    • Machine Learning Models

    • Viral Single-Cell Analysis

      • scViroCap - Single-cell viral capture sequencing analysis. [Python]
      • scVIRseq - Single-cell virus infection profiling. [Python]
      • Viral-Track - Tracking viruses in single-cell RNA-Seq data. [R]
      • MAVERIC - Analyzing viral infections at the single-cell level. [Python]

    • Viral Glycoprotein Analysis

      • GlycoProtViz - Visualizing viral glycoprotein structures. [Python]
      • GlyConnect - Database with viral glycosylation data. [web service]
      • NetNGlyc - N-glycosylation site prediction in viral proteins. [web service]
      • pGlyco - Glycopeptide identification in viral proteins. [C++]

    • Ancient Viral Sequence Analysis

      • EVE - Ancient viral element detection in genomes. [Python]
      • HOPS - Pathogen screening for ancient DNA, includes viral sequences. [Java]
      • Paleovirology - Tools for detecting ancient viral elements. [Perl]
      • PastML - Useful for ancient viral sequence reconstruction. [Python]

    • Viral Immune Epitope Prediction

      • EpiDOCK - Viral epitope docking and analysis. [web service]
      • IEDB-tools - Suite of tools for epitope prediction. [Python]
      • NetMHCpan - Neural network for MHC binding prediction in viral proteins. [web service]
      • TepiTool - T-cell epitope prediction for viral sequences. [web service]

    • Viral Molecular Dynamics

      • CHARMM-GUI - Web-based interface for viral particle simulation setup. [web service]
      • CovidMD - COVID-19 specific molecular dynamics toolbox (extensible to other viruses). [C++]
      • NAMD-VIRAL - Molecular dynamics simulations of viral proteins. [C++]
      • VMD-Viral - Visualization of viral molecular dynamics. [C++]

    • Dark Matter Viral Analysis

Programming Languages
Python 91 Perl 12 C++ 11 Shell 10 Jupyter Notebook 8 HTML 7 C 6 Nextflow 5 R 5 Java 2
Categories
Virus and Phage Identification 124 Other Tools 61 Host Prediction 28 Genome Analysis 18 Functional Analysis 13 Taxonomy 12 Top Packages by Category 11 Databases 11 Sequence Databases 11 Popular Packages 4 Visualization and Infrastructure 4 Sequence Analysis 2 CRISPR Analysis 2 Tool Comparison Matrix 1 License 1 Interactive Dashboard 1 Acknowledgments 1 Tool Selection Guide 1
Sub Categories
Metagenome Analysis 103 Gene Finding 42 RNA Virus Identification 32 Integrated Viruses 17 Interaction Analysis 7 Dark Matter Viral Analysis 5 Viral Orthologous Groups 5 Viral Quasispecies Analysis 5 Viral Single-Cell Analysis 4 Evolutionary Analysis 4 Viral Glycoprotein Analysis 4 Genome Analysis 4 Machine Learning Models 4 Viral Immune Epitope Prediction 4 Viral Molecular Dynamics 4 Ancient Viral Sequence Analysis 4 Structural Analysis Tools 4 Antimicrobial Resistance Analysis 4 Taxonomy 3 Genome Annotation 3 Host Prediction 3 Phage-specific Analysis 3 Cloud-based Viral Analysis 3 Lifestyle Classification 3 Viral Strain Reconstruction 3 Genome Completeness 3 Genome Comparison 2 Cyberinfrastructure 2 Viral Metatranscriptomics 2 Plaque Analysis 2 Genome Assembly 2 Simulation 2 Transduction 1 Amplicon Analysis 1 Sequence Translation 1 Virus and Phage Identification 1 Quality Control 1 Multiple Sequence Alignment 1
Keywords
bioinformatics 20 metagenomics 11 virus 10 genomics 8 virome 5 genome-assembly 5 nextflow 5 ngs 4 annotation 4 phages 4 snakemake 4 viral-metagenomics 4 virus-discovery 4 illumina 3 phage 3 nextflow-pipelines 3 python 3 virus-evolution 3 simulation 3 viral 3 cwl 3 prophage 3 bioinformatics-pipeline 3 evolution 3 genbank 3 ncbi 2 phage-sequences 2 phage-identification 2 phylogenetics 2 hiv 2 pipeline 2 sars-cov-2 2 workflow 2 sequence-analysis 2 viruses 2 next-generation-sequencing 2 genome 2 perl 2 nei-gojobori 2 natural-selection 2 molecular-evolution 2 dnds-estimation 2 dnds 2 scripts 2 hi-c 2 machine-learning 2 viral-metagenomes 2 virus-sequences 2 comparative-genomics 2 prophage-prediction 2