# | Title | Journal | Year | Citations |
---|
1 | RDP4: Detection and analysis of recombination patterns in virus genomes | Virus Evolution | 2015 | 2,621 |
2 | Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 | Virus Evolution | 2018 | 2,401 |
3 | Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) | Virus Evolution | 2016 | 1,638 |
4 | TreeTime: Maximum-likelihood phylodynamic analysis | Virus Evolution | 2018 | 883 |
5 | Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool | Virus Evolution | 2021 | 774 |
6 | Temporal signal and the phylodynamic threshold of SARS-CoV-2 | Virus Evolution | 2020 | 317 |
7 | Global patterns in coronavirus diversity | Virus Evolution | 2017 | 310 |
8 | RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets | Virus Evolution | 2021 | 257 |
9 | Editorial: A home for virology, ecology, epidemiology, and evolutionary biology | Virus Evolution | 2015 | 242 |
10 | Antiviral drug resistance as an adaptive process | Virus Evolution | 2016 | 162 |
11 | Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation | Virus Evolution | 2020 | 124 |
12 | An emergent clade of SARS-CoV-2 linked to returned travellers from Iran | Virus Evolution | 2020 | 119 |
13 | Scalable relaxed clock phylogenetic dating | Virus Evolution | 2017 | 116 |
14 | Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases | Virus Evolution | 2016 | 105 |
15 | Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages | Virus Evolution | 2020 | 104 |
16 | Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae | Virus Evolution | 2017 | 93 |
17 | An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain | Virus Evolution | 2022 | 93 |
18 | The diversification of begomovirus populations is predominantly driven by mutational dynamics | Virus Evolution | 2017 | 92 |
19 | Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code | Virus Evolution | 2018 | 90 |
20 | Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks | Virus Evolution | 2016 | 87 |
21 | In vivo mutation rates and the landscape of fitness costs of HIV-1 | Virus Evolution | 2017 | 85 |
22 | No evidence for distinct types in the evolution of SARS-CoV-2 | Virus Evolution | 2020 | 85 |
23 | Challenges in the analysis of viral metagenomes | Virus Evolution | 2016 | 83 |
24 | Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes | Virus Evolution | 2016 | 83 |
25 | Cenote-Taker 2 democratizes virus discovery and sequence annotation | Virus Evolution | 2021 | 82 |
26 | The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization | Virus Evolution | 2020 | 81 |
27 | Emergence of norovirus strains: A tale of two genes | Virus Evolution | 2019 | 77 |
28 | The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK | Virus Evolution | 2022 | 75 |
29 | The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study | Virus Evolution | 2016 | 69 |
30 | The evolution, diversity, and host associations of rhabdoviruses | Virus Evolution | 2015 | 68 |
31 | HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries | Virus Evolution | 2016 | 68 |
32 | Intra-host evolution during SARS-CoV-2 prolonged infection | Virus Evolution | 2021 | 68 |
33 | The virome of Drosophila suzukii, an invasive pest of soft fruit | Virus Evolution | 2018 | 67 |
34 | Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver | Virus Evolution | 2018 | 64 |
35 | Viral coinfection is shaped by host ecology and virus–virus interactions across diverse microbial taxa and environments | Virus Evolution | 2017 | 63 |
36 | Co-circulation of genetically distinct highly pathogenic avian influenza A clade 2.3.4.4 (H5N6) viruses in wild waterfowl and poultry in Europe and East Asia, 2017–18 | Virus Evolution | 2019 | 63 |
37 | Novel hepatitis D-like agents in vertebrates and invertebrates | Virus Evolution | 2019 | 63 |
38 | The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses | Virus Evolution | 2018 | 61 |
39 | MERS-CoV recombination: implications about the reservoir and potential for adaptation | Virus Evolution | 2016 | 60 |
40 | Host ecology determines the dispersal patterns of a plant virus | Virus Evolution | 2015 | 59 |
41 | The global distribution ofBanana bunchy top virusreveals little evidence for frequent recent, human-mediated long distance dispersal events | Virus Evolution | 2015 | 58 |
42 | Virome composition in marine fish revealed by meta-transcriptomics | Virus Evolution | 2021 | 58 |
43 | Role of the host restriction factor APOBEC3 on papillomavirus evolution | Virus Evolution | 2015 | 57 |
44 | The phylogenetics of the global population of potato virus Y and its necrogenic recombinants | Virus Evolution | 2017 | 57 |
45 | Viral invasion fitness across a continuum from lysis to latency† | Virus Evolution | 2019 | 57 |
46 | Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains | Virus Evolution | 2018 | 56 |
47 | Interannual dynamics, diversity and evolution of the virome in Sclerotinia sclerotiorum from a single crop field | Virus Evolution | 2021 | 56 |
48 | Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing | Virus Evolution | 2015 | 55 |
49 | Understanding the evolution and spread of chikungunya virus in the Americas using complete genome sequences | Virus Evolution | 2017 | 55 |
50 | Diverse and highly recombinant anelloviruses associated with Weddell seals in Antarctica | Virus Evolution | 2017 | 55 |