This table of links is interactive: keyword search can be performed in the search box and combined.
For example "HBV" will list the links releant to this virus, or "HIV drug" the sites related to the drugs against HIV.

Sites Comment Interface Specificity
dsRNA viruses resource various information about taxonomy, outbreaks and sequences of dsRNA viruses web(last update 2009) Reoviridae, Cystoviridae, Birnaviridae, Totiviridae
Reference Center for bacterial viruses Collects, conserves and distributes reference phages and information. web phages
ACLAME database dedicated to the collection and classification of mobile genetic elements (MGEs) web phages
Bioafrica.net research, software and publications based on HIV, HCV and few other viruses web HIV, HCV, HPV
UCSC Ebola Genome Portal Collection on data on the 2014 ebola outbreak web Ebolavirus
BROAD institute Dengue virus database Dengue virus sequences and analysis tools web Dengue
Virology blog Blog focussed on virus molecular biology web All viruses
NetPicoRNA Prediction of picornaviridae cleavage sites on amino acid sequences web Picornaviridae
NetCorona Prediction of Coronavirus 3CL Proteinase cleavage sites on amino acid sequences web Coronaviridae
VirusWorld Virus capsids pictures and movies web All viruses
Retroviruses Detailed knowledge on Retrovirus molecular biology Online book Retroviridae, HIV
INTRINSIC STRUCTURE OF VIRUS CAPSIDS Details on capsid structure and nomenclature Online book all viruses
Iterative Virus Assembler (IVA) tool to assemble virus genomes from NGS/metagenomics download metagenome
Baculovirus molecular biology Detailled knowledge on baculovirus molecular biology Online book Baculovirus
Virology.ca Databases and resources for viral genomics web Asfarviridae, Herpesviridae, Poxviridae, Iridoviridae, Baculoviridae
UniProt protein sequences of all public viral ORF web All viruses
RNA virus database Sequence analysis tools and data for RNA viruses web RNA viruses
HIV-1 databases sequence, vaccine, drug resistance and immunology databases web HIV-1
IRESite database of experimentally verified IRES structures web Picornaviridae, Flaviviridae, Discistroviridae, Retroviridae, Tombusviridae
Database of Bat-associated Viruses (DBatVir) Bat viruses with details about their hosts and location web Bat viruses
European society for virology Society promoting discussion and collaboration among scientists, organizing a congress every three years web All viruses
American society for virology Society promoting discussion and collaboration among scientists, organizing an annual congress web all viruses
Plant viruses online Classification, hosts and symptoms of plant viruses web Plant viruses
Virology history description og historical developments that led to the determination of the structure and biological functions of viruses web Picornaviridae, Influenzavirus, plant viruses
Giantvirus.org Resource on mimivirus (last update 2005) web Mimivirus, pandoravirus
Microbewiki: viral bioreaml student-edited microbiology resource web all viruses
All the virology on the www links to virology resources on the web web all viruses
ATIVS Analysis tools for influenza virus surveillance web Influenza virus
AVPdb Human viruses Resource of experimentally validated antiviral peptides web Human viruses
AVPpred Antiviralpeptide prediction algorythm web all viruses
Base-By-Base Software package to identify differences between genomes download all viruses
bNAber Database of broadly neutralizing HIV antibodies web HIV
CAPIH comparative host HIV-1 protein interaction network between human and model animals web HIV
CoVDB Repository of annotated coronavirus genes/genomes web Coronavirus
DengueNet For a global surveillance of Dengue fever and Dengue haemorrhagic fever web Dengue virus
Description of plant viruses (DPV) Information about viruses, viroids and satellites of plants, fungi and protozoa. web Plant, funghi, protozoa viruses
Dr.VIS Catalogs human disease-related viral integration sites web Human viruses
EpiFlu Comprehensive collection of Influenza sequences containing associated clinical/epidemiological metadata Web (login) Influenza virus
euHCVdb Resource computer-annotated sequences, protein sequences/structures and functional analyses tools (now succeeded by ViPR) web Hepatitis C virus
EuResist For predicting response to anti-HIV therapy web or download HIV
FLAVIdB Web portal combining antigenic data of flaviviruses and analysis tools web Flaviviruses
Flavitrack Manually annotated database of flavivirus sequences Inaccessible, Dec14 Flaviviruses
FluGenome For genotypoing influenza A virus and analyzing reassortment events web Influenza virus
FluTE Influenza epidemic simulation model download Influenza virus
GATU (Genome Annotation Transfer Utility) Annotation of viral genomes web all viruses
Geno2pheno For predicting drug resistance in HIV-1, HBV and HCV web HIV-1, HBV and HCV
GIB-V Platform for comparative analysis of viral genomes Inaccessible dec14
GiRaF Identification of influenza reassortments download Influenza virus
HBVdb Provides access to computer-annotated sequences as well as generic (BLAST, FASTA, ClustalW) and specialized tools for annotation, genotyping and drug resistance profiling web HBV
HBVPathDB Pathway information of HBV infection-related reactions Inaccessible dec14 HBV
HBVRegDB Database for detection of regulatory elements web HBV
HepSEQ Hosts molecular, clinical and epidemiological information as well as Sequence Matcher, Genotyper and Polymerase Annotator tools for HBV web HBV
HERVd Repository of human endogenous retroviruses web HERV
HESAS Database to understand the role of HERVs in the human genome web HERV
HIPdb Repository of experimentally validated HIV inhibiting peptides web HIV
HIVCD Tool for contamination screening in HIV sequence laboratory download HIV
HIV Positive Selection Mutation DB Selection pressure maps of HIV protease and reverse transcriptase web HIV
HIVSIM For comparing effectiveness of novel HIV therapy regimens download HIV
HIVsirDB Repository of HIV inhibiting siRNAs web HIV
HIV Systems Biology Houses Gene Overlapper, Replication Cycle site, GPS-Prot and AIDSVu tools web HIV
HPV-QUEST Tool for genotyping HPV web HPV
HTLV-1 Molecular Epidemiology DB For HTLV-1 sequence management and data mining web HTLV
HVDB Database of hepatitis A/B/C/D/E virus sequences as well as provides a phylogenetic analysis tool web HAV, HBV, HCV, HDV, HEV
ICTV Taxonomic classification and nomenclature of viruses web all viruses
IPDR Designing primers/probes for influenza diagnostics web Influenza virus
IRD Resource of influenza virus host-pathogen interactions as well web Influenza virus
ISED Catalogs influenza sequence and epitope information of viruses from Asia web Influenza virus
IVDB Hosts influenza sequence data, Q-filter system as well as BLAST, alignment, phylogenetic and sequence distribution tools web Influenza virus
jpHMM To analyze recombinations in viruses web and download HIV, HBV
LANL HCV Database Contains sequence data and immunological epitopes in HCV (now succeeded by ViPR) web HCV
LANL HFV Database Houses annotated Hemorrhagic Fever Viruses sequences and several analysis tools web Hemorrhagic Fever Viruses
LANL HIV Database2 Comprehensive resource on HIV sequences, immunological epitopes, drug resistance and vaccine trials web HIV
LearnCoil-VMF Identifying coiled-coil-like motifs in viral membrane-fusion proteins web all viruses
Metavir Web server for analysis of viral metagenomes (viromes) web metagenome
NCBI Genotyping Tool Resource for genotyping of viral sequences web HIV, HBV, HTLV, Poliovirus
NCBI HIV-1, Human Interaction Database Catalogs all interactions between HIV-1 and human proteins web HIV
NCBI Influenza Resource Influenza virus standardized annotation, metadata based sequence retrieval and analysis tools web Influenza virus
NCBI Viral Genome Resource Catalogue of all viral genomes with their proteins and references for all viral species. Contains more that 70,000 genomes web all viruses
NCBI Virus Variation Resource Ebolavirus, MERS coronavirus, Dengue, West Nile-standardized annotation, metadata based sequence retrieval and analysis tools web Ebolavirus, MERS coronavirus, Dengue, West Nile virus
OpenFluDB Isolate-centric database for influenza virus (contains information about virus type, host and collection date/place) web Influenza virus
Paparazzi Perl script to reconstruct entire viral genome from virus-derived siRNAs Inaccessible, Fev15 NGS
PaVE Hosts annotated papillomavirus genomes and protein sequence/structures web HPV
PBRC Comprehensive Poxviridae informational and analytical resource (now merged into ViPR) web Poxviridae
PHACCS To assess the diversity of uncultured/environmental viral communities download metagenome
PhEVER Houses evolutionary and phylogenetic information to analyze the nature of virus-virus and virus-host lateral gene transfers web all viruses
phiSITE Database of gene regulation in bacteriophages web phages
PhyloType To analyze large phylogenies web and download Phylogeny
PIRSpred For HIV-1 protein-inhibitor resistance/susceptibility prediction web HIV
PrimerHunter Primer designing tool for virus subtyping web and download all viruses
PriSM Tool to select optimal primers for amplification of viral genomes web all viruses
RetroTector Detection of retroviral sequences in vertebrate genomes web Retroviridae
RNA Virus Database Devoted to RNA viruses web RNA viruses
RotaC Genotyping tool for group A rotaviruses web Rotavirus
SCUEAL Prediction of HIV-1 subtypes web HIV
SeqMap 2.0 Identifying integration sites from LM-PCR, LAM-PCR and nrLAM-PCR analysis web Integrated virus
siVirus Antiviral siRNA design software web HIV, SARS, Influenza, HCV
SQUAT Examining the quality of HIV-1 PR/RT sequences download HIV
SSE Nucleotide and amino acid sequence analysis platform download all viruses
Stanford HIV Drug Resistance DB Contains genotype-treatment, genotype-phenotype and genotype-outcome correlation data web HIV
STAR Subtyping tool for HIV-1 and HBV web HIV, HBV
Subviral RNA Database For research/analysis of viroids, satellite RNAs, satellites viruses and human hepatitis delta virus web RNA viruses
SugarBind Pathogen glucide/carbohydrate-binding database web
VaZyMolO BLAST tool for defining/classifying viral protein modules web all viruses
VBRC Viral resource of informational and analytical tools (now merged into ViPR) web Arenaviridae, Bunyaviridae, Flaviridae, Filoviridae, Paramyxoviridae, Poxviridae, Togaviridae
vFitness To estimate HIV-1 fitness (replication rate) web HIV
VGO Annotation of complete viral genomes especially large poxviruses web poxviridae
VIDA Organizes homologous protein families from animal virus genomes web Arteriviridae, Poxviridae, Coronaviridae, Herpesviridae, Papillomaviridae
VIGOR Gene prediction program web RNA viruses
VIPERdb Database for icosahedral virus capsid structures web All viruses
ViPR Integrated repository of data (sequences, protein structures, epitopes, clinical/surveillance metadata) and analysis tools (BLAST, alignment, phylogeny) for multiple virus families web Caliciviridae, Coronaviridae, Flaviviridae, Hepeviridae, Picornaviridae, Togaviridae, Arenaviridae, Bunyaviridae, Filoviridae, Paramyxoviridae, Rhabdoviridae, Reoviridae, Herpesviridae, Poxviridae
VIPR For detecting recombinant and non-recombinant viruses hybridized to diagnostic microarray download all viruses
Viral IRES Prediction System (VIPS) Prediction of viral IRESs web all viruses
ViralFusionSeq To discover integration events by combining soft-clipping information, read-pair analysis and targeted de novo assembly download all viruses
ViralZone Fact sheets on all known virus families/genera with sequence data web all viruses
VIRAPOPS Forward simulator to model specific RNA virus functions download RNA virus
ViReMa Algorithm for detection of recombination junctions in viral genomes download all viruses
VirHostNet Resource of virus-host interaction networks coupled to their functional annotation web all viruses
Vir-Mir db Catalogs potential viral miRNA hairpins and allows prediction of viral miRNA target genes web all viruses
ViroBLAST Extends utility of BLAST to query against multiple databases and user-customized datasets web and download all viruses
VirOligo Repository of virus-specific oligonucleotides web all viruses
VIROME Pipeline for classification of viral metagenomic sequences web metagenome
viRome R package for analysis of viral small RNA sequence datasets download all viruses
VIRsiRNAdb Curated database of siRNA/shRNA targeting 42 important human viruses web Human viruses
VIRsiRNApred Viral siRNA efficacy prediction tool web all viruses
VirusFinder Software for detecting integration sites by blending SVdetect with CREST download NGS
Virus-Genotyping Tools High-throughput genotyping of recombinant and nonrecombinant viruses web HIV, HTLV, HBV, HCV, KSHV, HPV
VirusHunter Pipeline for detection of novel/known viruses from various specimens download metagenome
VirusMINT Hosts interactions between viral and human proteins web
VirusSeq For finding integration events using discordant read-pair information download all viruses
Visitor Perl script for analysis of viral siRNA datasets from Illumina sequencing platform download Drosphila viruses
ViTa Houses known host/viral miRNAs and known/putative host miRNA targets web all viruses
VMGAP Pipeline for functional annotation of metagenomic data method metagenome
ZCURVE_V Gene-finding tool for viral genomes web and download all viruses
Paleovirology This website aims to provide a stable repository for the endogenous viruses, and provides paleovirus reference sequences for retroviruses web all endogenous viruses
ViRBase visualization of virus-host ncRNA-associated interactions and interaction networks in viral infection web all viruses
ViRAD Virus (re-)annotation database; adds newly identified ORFs to virus sequences web all viruses
VirAmp fast virus genome assembly pipeline designed for extremely high coverage NGS data web all viruses
PaVE Papillomavirus Episteme: resource with reference sequences, annotation and analysis tools web Papillomaviruses
VirusDetect An automated pipeline for efficient virus discovery using deep sequencing of small RNAs. web Plant viruses
ScienceofHIV Animation showing some key steps of HIV life cycle Web HIV


Sources:
-Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research
For further details and to compare/select the most suitable tools to carry out a desired task refer to the aforementioned paper.
-2014 NAR Database Summary Paper