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Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny

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The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

Statistics and Truth in Phylogenomics

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Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

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Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

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Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited

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The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

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Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

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Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi

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Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

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Phylogenomics Revives Traditional Views on Deep Animal Relationships

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Large-Scale Parsimony Analysis of Metazoan Indels in Protein-Coding Genes

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Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

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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

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

(2009) Bernd Schierwater et al.   PLOS BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

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Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence

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