Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

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

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?

(2009) Flor Rodriguez et al.   BMC EVOLUTIONARY BIOLOGY

Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples

(2009) Michael DeGiorgio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

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

What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?

(2009) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Species Tree Discordance Traces to Phylogeographic Clade Boundaries in North American Fence Lizards (Sceloporus)

(2009) Adam D. Leaché   SYSTEMATIC BIOLOGY

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

(2009) Laura Salter Kubatko   SYSTEMATIC BIOLOGY

Species Trees from Highly Incongruent Gene Trees in Rice

(2009) Karen A. Cranston et al.   SYSTEMATIC BIOLOGY

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

(2009) L. Lacey Knowles   SYSTEMATIC BIOLOGY

Properties of Consensus Methods for Inferring Species Trees from Gene Trees

(2009) James H. Degnan et al.   SYSTEMATIC BIOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Species Tree Inference by Minimizing Deep Coalescences

(2009) Cuong Than et al.   PLoS Computational Biology

Fine-Scale Phylogenetic Discordance across the House Mouse Genome

(2009) Michael A. White et al.   PLoS Genetics

AUGIST: inferring species trees while accommodating gene tree uncertainty

(2008) J. C. Oliver   BIOINFORMATICS

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

Using supernetworks to distinguish hybridization from lineage-sorting

(2008) Barbara R Holland et al.   BMC EVOLUTIONARY BIOLOGY

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs

(2008) J. E. Horvath et al.   GENOME RESEARCH

Revisiting horizontal transfer of transposable elements in Drosophila

(2008) E L S Loreto et al.   HEREDITY

Subdivision in an Ancestral Species Creates Asymmetry in Gene Trees

(2008) M. Slatkin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dealing with incongruence in phylogenomic analyses

(2008) N. Galtier et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparison of Species Tree Methods for Reconstructing the Phylogeny of Bearded Manakins (Aves: Pipridae, Manacus) from Multilocus Sequence Data

(2008) Robb T. Brumfield et al.   SYSTEMATIC BIOLOGY

Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae)

(2008) Natalia M. Belfiore et al.   SYSTEMATIC BIOLOGY

The Reticulate History of Medicago (Fabaceae)

(2008) Iván J. Maureira-Butler et al.   SYSTEMATIC BIOLOGY

Discordance of Species Trees with Their Most Likely Gene Trees: The Case of Five Taxa

(2008) Noah A. Rosenberg et al.   SYSTEMATIC BIOLOGY

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY