Ultrafast Approximation for Phylogenetic Bootstrap

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods

(2011) Minh Anh Thi Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

Characterizing the Phylogenetic Tree-Search Problem

(2011) Daniel Money et al.   SYSTEMATIC BIOLOGY

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Prevalence of Multifurcations in Tree-space and Their Implications for Tree-search

(2010) Simon Whelan et al.   MOLECULAR BIOLOGY AND EVOLUTION

MISFITS: Evaluating the Goodness of Fit between a Phylogenetic Model and an Alignment

(2010) Minh Anh Thi Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY