TreeKnit: Inferring ancestral reassortment graphs of influenza viruses

Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

(2020) Nicola F. Müller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Fitness cost of reassortment in human influenza

(2017) Mara Villa et al.   PLoS Pathogens

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1–PB2–HA Gene Complex

(2014) Gytis Dudas et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes

(2014) Alexey D. Neverov et al.   PLoS Genetics

New approaches for unravelling reassortment pathways

(2013) Victoria Svinti et al.   BMC EVOLUTIONARY BIOLOGY

A comprehensive analysis of reassortment in influenza A virus

(2012) U. C. de Silva et al.   Biology Open

FluReF, an automated flu virus reassortment finder based on phylogenetic trees

(2011) Alisa Yurovsky et al.   BMC GENOMICS

Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations

(2011) R. A. Neher et al.   GENETICS

Why do RNA viruses recombine?

(2011) Etienne Simon-Loriere et al.   NATURE REVIEWS MICROBIOLOGY

GiRaF: robust, computational identification of influenza reassortments via graph mining

(2010) Niranjan Nagarajan et al.   NUCLEIC ACIDS RESEARCH

The emergence of pandemic influenza viruses

(2010) Yi Guan et al.   Protein & Cell

Extended Newick: it is time for a standard representation of phylogenetic networks

(2009) Gabriel Cardona et al.   BMC BIOINFORMATICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dating the emergence of pandemic influenza viruses

(2009) Gavin J. D. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-random reassortment in human influenza A viruses

(2008) Raul Rabadan et al.   Influenza and Other Respiratory Viruses

Multiple Reassortment Events in the Evolutionary History of H1N1 Influenza A Virus Since 1918

(2008) Martha I. Nelson et al.   PLoS Pathogens