Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genome Comparison of Candida orthopsilosis Clinical Strains Reveals the Existence of Hybrids between Two Distinct Subspecies

(2014) Leszek P. Pryszcz et al.   Genome Biology and Evolution

Preservation of genetic and regulatory robustness in ancient gene duplicates ofSaccharomyces cerevisiae

(2014) Orla M. Keane et al.   GENOME RESEARCH

A phylogenomics approach for selecting robust sets of phylogenetic markers

(2014) Salvador Capella-Gutierrez et al.   NUCLEIC ACIDS RESEARCH

Sequencing and Characterisation of Rearrangements in Three S. pastorianus Strains Reveals the Presence of Chimeric Genes and Gives Evidence of Breakpoint Reuse

(2014) Sarah K. Hewitt et al.   PLoS One

Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach

(2013) Charles-Elie Rabier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Whole Genome Duplication and Enrichment of Metal Cation Transporters Revealed by De Novo Genome Sequencing of Extremely Halotolerant Black Yeast Hortaea werneckii

(2013) Metka Lenassi et al.   PLoS One

How old is my gene?

(2013) John A. Capra et al.   TRENDS IN GENETICS

Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus

(2012) Marina Marcet-Houben et al.   BMC GENOMICS

Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts

(2012) Lucia Morales et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Pichia sorbitophila , an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization

(2012) Véronique Leh Louis et al.   G3-Genes Genomes Genetics

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

The genome sequence of the wine yeast VIN7 reveals an allotriploid hybrid genome with Saccharomyces cerevisiae and Saccharomyces kudriavzevii origins

(2011) Anthony R. Borneman et al.   FEMS YEAST RESEARCH

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Assigning duplication events to relative temporal scales in genome-wide studies

(2010) J. Huerta-Cepas et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence

(2009) Marina Marcet-Houben et al.   BMC EVOLUTIONARY BIOLOGY

Ploidy and the Causes of Genomic Evolution

(2009) A. C. Gerstein et al.   JOURNAL OF HEREDITY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

(2009) Marina Marcet-Houben et al.   PLoS One

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

(2009) Li-Jun Ma et al.   PLoS Genetics

Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

(2009) Jonathan L. Gordon et al.   PLoS Genetics

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

“Changing by doubling”, the impact of Whole Genome Duplications in the evolution of eukaryotes

(2008) Olivier Jaillon et al.   COMPTES RENDUS BIOLOGIES

Interspecies hybridization and recombination inSaccharomyceswine yeasts

(2008) Matthias Sipiczki   FEMS YEAST RESEARCH

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

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