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nextflu specifications


Unique identifier OMICS_09372
Name nextflu
Interface Web user interface
Restrictions to use None
Programming languages Javascript, Python
License GNU Affero General Public License version 3
Computer skills Basic
Stability Stable
Maintained Yes


  • Viruses
    • Influenza A virus
    • Influenza A virus (A/Puerto Rico/8/1934(H1N1))
    • Influenza B virus




  • person_outline Trevor Bedford

Publication for nextflu

nextflu citations


TreeTime: Maximum likelihood phylodynamic analysis

Virus Evol
PMCID: 5758920
PMID: 29340210
DOI: 10.1093/ve/vex042

[…] TreeTime was developed to analyse large heterochronous viral sequence alignments and we have used TreeTime as the core component of the real-time phylogenetics pipelines nextstrain and nextflu (). TreeTime tries to strike a useful compromise between inflexible but fast heuristics and computationally expensive Bayesian approaches that require extensive sampling of treespace. The over […]


Genome wide evolutionary dynamics of influenza B viruses on a global scale

PLoS Pathog
PMCID: 5790164
PMID: 29284042
DOI: 10.1371/journal.ppat.1006749

[…] t to the serial replacement of novel antigenic types in the Victoria-lineage viruses (), the two antigenically-distinct clades of the Yamagata-lineage co-circulate globally, alternating in dominance ( (). However, despite the divergence and counter-cyclical maintenance of Yamagata-lineage clades 2 and 3 over 10 years, recent reports indicate that the incidence of clade 2 virus […]


Rules of co occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses

BMC Med Genomics
PMCID: 5260787
PMID: 28117657
DOI: 10.1186/s12920-016-0230-5

[…] e dynamics of antigenic evolution. The relationship between the antigenic distances based on sequences and those calculated from HI titer data was further discussed in [], where an online tool named “nextflu” was provided for real-time tracking. Although those studies have obtained insightful results, most of them focus on the clusters of antigenic mutations. Currently very few studies work on the […]


Virus genomics and evolution: the transformative effect of new technologies and multidisciplinary collaboration on virus research and outbreak management

Genome Biol
PMCID: 4960802
PMID: 27457219
DOI: 10.1186/s13059-016-1019-8

[…] t, from sourcing nitrogen canisters to managing samples, must not be underestimated. Ian demonstrated the benefits of sharing, whether it be of open-access data via platforms like and or of the sequencing equipment itself, which was eventually rehomed at the University of Makeni. Hinting at a subject that might feature at the next edition of the conference, Oliver Pybus […]


Real time digital pathogen surveillance — the time is now

Genome Biol
PMCID: 4531805
PMID: 27391693
DOI: 10.1186/s13059-015-0726-x

[…], make it easy for international teams to write to an ‘open lab notebook’ []. Online tools can provide powerful evolutionary and epidemiological visualizations, such as Bedford and Nehrer’s nextflu, which was originally designed for influenza strain tracking and has now been adapted to integrate real-time Ebola genomic datasets ( []. We have also employed the Mic […]


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nextflu institution(s)
Max Planck Institute for Developmental Biology, Tübingen, Germany; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
nextflu funding source(s)
This work was supported by the ERC though Stg-260686 and by the NIH through U54 GM111274.

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