Efficient Exploration of the Space of Reconciled Gene Trees

Lateral Gene Transfer from the Dead

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

The Estimation of Tree Posterior Probabilities Using Conditional Clade Probability Distributions

(2013) Bret Larget   SYSTEMATIC BIOLOGY

Unified modeling of gene duplication, loss, and coalescence using a locus tree

(2012) M. D. Rasmussen et al.   GENOME RESEARCH

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

(2012) G. J. Szollosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees

(2012) Yi-Chieh Wu et al.   SYSTEMATIC BIOLOGY

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

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

Guided Tree Topology Proposals for Bayesian Phylogenetic Inference

(2011) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

Dating the cyanobacterial ancestor of the chloroplast

(2010) Luisa I Falcón et al.   ISME Journal

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

(2009) O. Akerborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomes as documents of evolutionary history

(2009) Bastien Boussau et al.   TRENDS IN ECOLOGY & EVOLUTION

Birth-death prior on phylogeny and speed dating

(2008) Orjan Akerborg et al.   BMC EVOLUTIONARY BIOLOGY

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION