Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference

Model selection may not be a mandatory step for phylogeny reconstruction

(2019) Shiran Abadi et al.   Nature Communications

Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale

(2017) Charles S.P. Foster et al.   Genome Biology and Evolution

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families

(2017) David A Duchêne et al.   SYSTEMATIC BIOLOGY

More on the Best Evolutionary Rate for Phylogenetic Analysis

(2017) Seraina Klopfstein et al.   SYSTEMATIC BIOLOGY

An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times

(2017) Konstantinos Angelis et al.   SYSTEMATIC BIOLOGY

The impacts of drift and selection on genomic evolution in insects

(2017) K. Jun Tong et al.   PeerJ

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Mammalian genome evolution is governed by multiple pacemakers

(2015) Sebastián Duchêne et al.   BIOINFORMATICS

The Effects of Partitioning on Phylogenetic Inference

(2015) David Kainer et al.   MOLECULAR BIOLOGY AND EVOLUTION

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Universal Pacemaker of Genome Evolution in Animals and Fungi and Variation of Evolutionary Rates in Diverse Organisms

(2014) Sagi Snir et al.   Genome Biology and Evolution

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages

(2014) Simon Y. W. Ho et al.   Molecular Ecology Resources

Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data

(2014) Sebastián Duchêne et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci

(2014) Tianqi Zhu et al.   SYSTEMATIC BIOLOGY

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

The changing face of the molecular evolutionary clock

(2014) Simon Y.W. Ho   TRENDS IN ECOLOGY & EVOLUTION

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

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

Universal Pacemaker of Genome Evolution

(2012) Sagi Snir et al.   PLoS Computational Biology

The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates

(2011) Brandon Gaut et al.   Annual Review of Ecology Evolution and Systematics

Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data

(2011) AKIFUMI S. TANABE   Molecular Ecology Resources

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets

(2010) Arong Luo et al.   BMC EVOLUTIONARY BIOLOGY

Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks

(2010) Simon Y. W. Ho et al.   Mitochondrial DNA

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Overdispersion of the Molecular Clock: Temporal Variation of Gene-Specific Substitution Rates in Drosophila

(2008) T. Bedford et al.   MOLECULAR BIOLOGY AND EVOLUTION