Searching for virus phylotypes

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Origin and Evolutionary History of HIV-1 Subtype C in Senegal

(2012) Matthieu Jung et al.   PLoS One

Molecular Epidemiology of HIV-1 Subtypes in India: Origin and Evolutionary History of the Predominant Subtype C

(2012) Ujjwal Neogi et al.   PLoS One

Global trends in molecular epidemiology of HIV-1 during 2000–2007

(2011) Joris Hemelaar et al.   AIDS

High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America

(2011) N. M. C. Veras et al.   JOURNAL OF GENERAL VIROLOGY

Origin and Dynamics of HIV-1 Subtype C Infection in India

(2011) Chengli Shen et al.   PLoS One

Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning

(2011) Michael M. Thomson et al.   VIROLOGY

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues

(2010) Susanna L. Lamers et al.   INFECTION GENETICS AND EVOLUTION

The HIV-1 Subtype C Epidemic in South America Is Linked to the United Kingdom

(2010) Tulio de Oliveira et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities

(2009) Thomas Pommier et al.   BIOINFORMATICS

Demonstration of Sustained Drug-Resistant Human Immunodeficiency Virus Type 1 Lineages Circulating among Treatment-Naive Individuals

(2009) S. Hue et al.   JOURNAL OF VIROLOGY

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

(2009) Sergei L. Kosakovsky Pond et al.   PLoS Computational Biology

Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation

(2008) Leonid Zaslavsky et al.   BMC BIOINFORMATICS

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

High-Resolution Molecular Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania

(2008) Marco Salemi et al.   PLoS One

Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis

(2008) Richard H. Ree et al.   SYSTEMATIC BIOLOGY