@article{neher_nextflu:_2015,
 abstract = {Seasonal influenza viruses evolve rapidly, allowing them to evade immunity in their human hosts and reinfect previously infected individuals. Similarly, vaccines against seasonal influenza need to be updated frequently to protect against an evolving virus population. We have thus developed a processing pipeline and browser-based visualization that allows convenient exploration and analysis of the most recent influenza virus sequence data. This web-application displays a phylogenetic tree that can be decorated with additional information such as the viral genotype at specific sites, sampling location and derived statistics that have been shown to be predictive of future virus dynamics. In addition, mutation, genotype and clade frequency trajectories are calculated and  displayed. AVAILABILITY AND IMPLEMENTATION: Python and Javascript source code is  freely available from https://github.com/blab/nextflu, while the web-application  is live at http://nextflu.org. CONTACT: tbedford@fredhutch.org.},
 area = {influenza_evolution, software},
 author = {Neher, Richard A. and Bedford, Trevor},
 code = {github.com/nextstrain/augur},
 copyright = {(c) The Author 2015. Published by Oxford University Press.},
 date = {2015-06-26},
 doi = {10.1093/bioinformatics/btv381},
 issn = {1367-4811 1367-4803},
 journal = {Bioinformatics (Oxford, England)},
 keywords = {Evolution, Molecular, Humans, Influenza, Human/*virology, Mutation, Orthomyxoviridae/classification/*genetics/isolation \& purification, Phylogeny, Seasons, Software},
 language = {eng},
 month = {November},
 number = {21},
 pages = {3546--3548},
 pdf = {neher_nextflu:_2015.pdf},
 pmcid = {PMC4612219},
 pmid = {26115986},
 projectpage = {nextflu.org},
 title = {nextflu: real-time tracking of seasonal influenza virus evolution in humans.},
 volume = {31},
 year = {2015}
}