Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps

(2015) Jakub Truszkowski et al.   SYSTEMATIC BIOLOGY

tqDist: a library for computing the quartet and triplet distances between binary or general trees

(2014) Andreas Sand et al.   BIOINFORMATICS

The top 100 papers

(2014) Richard Van Noorden et al.   NATURE

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylodynamics of HIV-1 Subtype C Epidemic in East Africa

(2012) Edson Oliveira Delatorre et al.   PLoS One

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

(2012) Andre J. Aberer et al.   SYSTEMATIC BIOLOGY

The origin and diversity of the HIV-1 pandemic

(2012) Joris Hemelaar   TRENDS IN MOLECULAR MEDICINE

A Metric for Phylogenetic Trees Based on Matching

(2011) Yu Lin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Statistics and Truth in Phylogenomics

(2011) S. Kumar 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

First-Order Correct Bootstrap Support Adjustments for Splits that Allow Hypothesis Testing When Using Maximum Likelihood Estimation

(2010) E. Susko   MOLECULAR BIOLOGY AND EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price 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

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

jpHMM: Improving the reliability of recombination prediction in HIV-1

(2009) A.-K. Schultz et al.   NUCLEIC ACIDS RESEARCH

Bootstrap Support Is Not First-Order Correct

(2009) Edward Susko   SYSTEMATIC BIOLOGY

Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

(2009) Robert C. Thomson et al.   SYSTEMATIC BIOLOGY

Using repeated measurements to validate hierarchical gene clusters

(2008) Laurent Bréhélin et al.   BIOINFORMATICS

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY