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Journal Article

FluMut: a tool for mutation surveillance in highly pathogenic H5N1 genomes

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Edoardo Giussani and others
Virus Evolution, Volume 11, Issue 1, 2025, veaf011, https://doi.org/10.1093/ve/veaf011
Published: 07 March 2025
Journal Article

SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period

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Nigam H Padhiar and others
Virus Evolution, Volume 11, Issue 1, 2025, veae115, https://doi.org/10.1093/ve/veae115
Published: 17 January 2025
Journal Article

F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny

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Yongtao Ye and others
Virus Evolution, Volume 10, Issue 1, 2024, veae056, https://doi.org/10.1093/ve/veae056
Published: 25 July 2024
Journal Article

Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus

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Sambit K Mishra and others
Virus Evolution, Volume 10, Issue 1, 2024, veae013, https://doi.org/10.1093/ve/veae013
Published: 07 February 2024
Journal Article

Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses

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Bin Ma and others
Virus Evolution, Volume 10, Issue 1, 2024, veae005, https://doi.org/10.1093/ve/veae005
Published: 27 January 2024
Journal Article

EvoLaps 2: Advanced phylogeographic visualization

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F Chevenet and others
Virus Evolution, Volume 10, Issue 1, 2024, vead078, https://doi.org/10.1093/ve/vead078
Published: 19 December 2023
Journal Article

HexSE: Simulating evolution in overlapping reading frames

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Laura Muñoz-Baena and others
Virus Evolution, Volume 9, Issue 1, 2023, vead009, https://doi.org/10.1093/ve/vead009
Published: 23 February 2023
Journal Article

bayroot: Bayesian sampling of HIV-1 integration dates by root-to-tip regression

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Roux-Cil Ferreira and others
Virus Evolution, Volume 9, Issue 1, 2023, veac120, https://doi.org/10.1093/ve/veac120
Published: 21 December 2022
Journal Article

A biophysical model of viral escape from polyclonal antibodies

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Timothy C Yu and others
Virus Evolution, Volume 8, Issue 2, 2022, veac110, https://doi.org/10.1093/ve/veac110
Published: 12 December 2022
Journal Article

SPREAD 4: online visualisation of pathogen phylogeographic reconstructions

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Kanika D Nahata and others
Virus Evolution, Volume 8, Issue 2, 2022, veac088, https://doi.org/10.1093/ve/veac088
Published: 26 September 2022
Journal Article

Identifying SARS-CoV-2 regional introductions and transmission clusters in real time

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Jakob McBroome and others
Virus Evolution, Volume 8, Issue 1, 2022, veac048, https://doi.org/10.1093/ve/veac048
Published: 16 June 2022
Journal Article

Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer

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Derek W Wright and others
Virus Evolution, Volume 8, Issue 1, 2022, veac023, https://doi.org/10.1093/ve/veac023
Published: 18 March 2022
Journal Article

Phycova — a tool for exploring covariates of pathogen spread

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Tim Blokker and others
Virus Evolution, Volume 8, Issue 1, 2022, veac015, https://doi.org/10.1093/ve/veac015
Published: 18 February 2022
Journal Article

Sequencing SARS-CoV-2 genomes from saliva

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Tara Alpert and others
Virus Evolution, Volume 8, Issue 1, 2022, veab098, https://doi.org/10.1093/ve/veab098
Published: 03 January 2022
Journal Article

CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes

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Roux-Cil Ferreira and others
Virus Evolution, Volume 7, Issue 2, December 2021, veab092, https://doi.org/10.1093/ve/veab092
Published: 08 November 2021
Journal Article

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

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Áine O’Toole and others
Virus Evolution, Volume 7, Issue 2, December 2021, veab064, https://doi.org/10.1093/ve/veab064
Published: 30 July 2021
Journal Article

LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data

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Ahmed Al Qaffas and others
Virus Evolution, Volume 7, Issue 1, January 2021, veab042, https://doi.org/10.1093/ve/veab042
Published: 23 April 2021
Journal Article

GRACy: A tool for analysing human cytomegalovirus sequence data

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Salvatore Camiolo and others
Virus Evolution, Volume 7, Issue 1, January 2021, veaa099, https://doi.org/10.1093/ve/veaa099
Published: 30 December 2020
Journal Article

Cenote-Taker 2 democratizes virus discovery and sequence annotation

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Michael J Tisza and others
Virus Evolution, Volume 7, Issue 1, January 2021, veaa100, https://doi.org/10.1093/ve/veaa100
Published: 30 December 2020
Journal Article

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types

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Ilya Plyusnin and others
Virus Evolution, Volume 6, Issue 2, July 2020, veaa091, https://doi.org/10.1093/ve/veaa091
Published: 02 December 2020