Assessing Approaches for Inferring Species Trees from Multi-Copy Genes

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

Fast Local Search for Unrooted Robinson-Foulds Supertrees

(2012) R. Chaudhary et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

Resolution of ray-finned fish phylogeny and timing of diversification

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

Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life

(2012) Laura A. Katz et al.   SYSTEMATIC BIOLOGY

The Evolution of Pharyngognathy: A Phylogenetic and Functional Appraisal of the Pharyngeal Jaw Key Innovation in Labroid Fishes and Beyond

(2012) P. C. Wainwright et al.   SYSTEMATIC BIOLOGY

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses

(2011) Pawel Górecki et al.   BMC BIOINFORMATICS

From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events

(2011) Louxin Zhang   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles

(2011) Yun Yu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences

(2011) Cuong V. Than et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

(2011) Edgar M. Medina et al.   JOURNAL OF MOLECULAR EVOLUTION

Reconciling Gene and Genome Duplication Events: Using Multiple Nuclear Gene Families to Infer the Phylogeny of the Aquatic Plant Family Pontederiaceae

(2011) Rob W. Ness et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

A simulation study comparing supertree and combined analysis methods using SMIDGen

(2010) M Shel Swenson et al.   Algorithms for Molecular Biology

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models

(2010) Mukul S Bansal et al.   BMC BIOINFORMATICS

iGTP: A software package for large-scale gene tree parsimony analysis

(2010) Ruchi Chaudhary et al.   BMC BIOINFORMATICS

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Deep Genomic-Scale Analyses of the Metazoa Reject Coelomata: Evidence from Single- and Multigene Families Analyzed Under a Supertree and Supermatrix Paradigm

(2010) Thérèse A. Holton et al.   Genome Biology and Evolution

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

(2010) M. D. Rasmussen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants

(2009) J.G. Burleigh et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The gene evolution model and computing its associated probabilities

(2009) Lars Arvestad et al.   JOURNAL OF THE ACM

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

(2009) L. Lacey Knowles   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

(2008) A. Wehe et al.   BIOINFORMATICS

The Impact of Reticulate Evolution on Genome Phylogeny

(2008) Robert G. Beiko et al.   SYSTEMATIC BIOLOGY

A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals

(2007) D. Penny et al.   MOLECULAR BIOLOGY AND EVOLUTION