TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees

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

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

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

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Jane: a new tool for the cophylogeny reconstruction problem

(2010) Chris Conow et al.   Algorithms for Molecular Biology

Simultaneous Identification of Duplications and Lateral Gene Transfers

(2010) A Tofigh et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

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

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

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

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

Sampling Trees from Evolutionary Models

(2010) Klaas Hartmann et al.   SYSTEMATIC BIOLOGY

Many-core algorithms for statistical phylogenetics

(2009) M. A. Suchard et al.   BIOINFORMATICS

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH