ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

Dissemination, divergence and establishment of H7N9 influenza viruses in China

(2015) Tommy Tsan-Yuk Lam et al.   NATURE

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Expansion of Genotypic Diversity and Establishment of 2009 H1N1 Pandemic-Origin Internal Genes in Pigs in China

(2014) H. Liang et al.   JOURNAL OF VIROLOGY

Probabilistic Graphical Model Representation in Phylogenetics

(2014) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

OutbreakTools: A new platform for disease outbreak analysis using the R software

(2014) Thibaut Jombart et al.   Epidemics

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Phylodynamics of H5N1 avian influenza virus in Indonesia

(2012) TOMMY TSAN-YUK LAM et al.   MOLECULAR ECOLOGY

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

(2012) Huangkai Zhang et al.   NUCLEIC ACIDS RESEARCH

A Format for Phylogenetic Placements

(2012) Frederick A. Matsen et al.   PLoS One

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Reassortment Events among Swine Influenza A Viruses in China: Implications for the Origin of the 2009 Influenza Pandemic

(2011) T. T.-Y. Lam et al.   JOURNAL OF VIROLOGY

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS