treespace : Statistical exploration of landscapes of phylogenetic trees

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees

(2016) Wen Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution

(2016) Michelle Kendall et al.   MOLECULAR BIOLOGY AND EVOLUTION

apex: phylogenetics with multiple genes

(2016) Thibaut Jombart et al.   Molecular Ecology Resources

Causes, consequences and solutions of phylogenetic incongruence

(2014) A. Som   BRIEFINGS IN BIOINFORMATICS

An Algorithm for Constructing Principal Geodesics in Phylogenetic Treespace

(2014) Tom M. W. Nye   IEEE-ACM Transactions on Computational Biology and Bioinformatics

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Looking for trees in the forest: summary tree from posterior samples

(2013) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

(2013) M. T. G. Holden et al.   GENOME RESEARCH

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees

(2012) John Chakerian et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

How to measure and test phylogenetic signal

(2012) Tamara Münkemüller et al.   Methods in Ecology and Evolution

Principal components analysis in the space of phylogenetic trees

(2011) Tom M. W. Nye   ANNALS OF STATISTICS

Statistics and Truth in Phylogenomics

(2011) S. Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Terraces in Phylogenetic Tree Space

(2011) M. J. Sanderson et al.   SCIENCE

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

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

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

A principal component analysis for trees

(2010) Burcu Aydın et al.   Annals of Applied Statistics

adephylo: new tools for investigating the phylogenetic signal in biological traits

(2010) Thibaut Jombart et al.   BIOINFORMATICS

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Picante: R tools for integrating phylogenies and ecology

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

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods

(2010) Borys Wróbel   JOURNAL OF APPLIED GENETICS

Putting phylogeny into the analysis of biological traits: A methodological approach

(2010) Thibaut Jombart et al.   JOURNAL OF THEORETICAL BIOLOGY

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

The prokaryotic tree of life: past, present…and future?

(2008) James O. McInerney et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources

Testing for phylogenetic signal in phenotypic traits: New matrices of phylogenetic proximities

(2007) Sandrine Pavoine et al.   THEORETICAL POPULATION BIOLOGY