Fast and accurate branch lengths estimation for phylogenomic trees

Genomic Support for a Moa–Tinamou Clade and Adaptive Morphological Convergence in Flightless Ratites

(2014) Allan J. Baker et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals

(2014) E. J. P. Douzery et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Combinatorics of distance-based tree inference

(2012) F. Pardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

(2011) Anne Kupczok et al.   Algorithms for Molecular Biology

Large-Scale Phylogenomic Analyses Indicate a Deep Origin of Primary Plastids within Cyanobacteria

(2011) Alexis Criscuolo et al.   MOLECULAR BIOLOGY AND EVOLUTION

SuperFine: Fast and Accurate Supertree Estimation

(2011) M. Shel Swenson et al.   SYSTEMATIC BIOLOGY

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY

Choosing among Partition Models in Bayesian Phylogenetics

(2010) Y. Fan et al.   MOLECULAR BIOLOGY AND EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

(2010) J. Gordon Burleigh et al.   SYSTEMATIC BIOLOGY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

(2009) Y. I. Wolf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Combinatorics of least-squares trees

(2008) R. Mihaescu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA