Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

Extending the Conserved Phylogenetic Core of Archaea Disentangles the Evolution of the Third Domain of Life

(2015) Céline Petitjean et al.   MOLECULAR BIOLOGY AND EVOLUTION

Big data and other challenges in the quest for orthologs

(2014) E. L. L. Sonnhammer et al.   BIOINFORMATICS

An Alternative Root for the Eukaryote Tree of Life

(2014) Ding He et al.   CURRENT BIOLOGY

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

(2014) Luca Pozzi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation

(2014) Kalliopi Trachana et al.   PLoS One

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

(2014) Liping Zeng et al.   Nature Communications

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

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

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

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

(2013) Jenna Morgan Lang et al.   PLoS One

Did Terrestrial Diversification of Amoebas (Amoebozoa) Occur in Synchrony with Land Plants?

(2013) Omar Fiz-Palacios et al.   PLoS One

A daily-updated tree of (sequenced) life as a reference for genome research

(2013) Hai Fang et al.   Scientific Reports

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi

(2012) Salvador Capella-Gutiérrez et al.   BMC BIOLOGY

The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins

(2012) F. Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

A Metric for Phylogenetic Trees Based on Matching

(2011) Yu Lin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

A Consistent Phylogenetic Backbone for the Fungi

(2011) I. Ebersberger et al.   MOLECULAR BIOLOGY AND EVOLUTION

TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees

(2011) Marina Marcet-Houben et al.   NUCLEIC ACIDS RESEARCH

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Comprehensive Phylogenetic Reconstruction of Amoebozoa Based on Concatenated Analyses of SSU-rDNA and Actin Genes

(2011) Daniel J. G. Lahr et al.   PLoS One

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

(2011) Christopher J. Creevey et al.   PLoS One

Release LTPs104 of the All-Species Living Tree

(2011) Raúl Munoz et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals

(2011) Xuming Zhou et al.   SYSTEMATIC BIOLOGY

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

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

High Frequency of Horizontal Gene Transfer in the Oceans

(2010) L. D. McDaniel et al.   SCIENCE

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

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

On the Diversity of Malaria Parasites in African Apes and the Origin of Plasmodium falciparum from Bonobos

(2010) Sabrina Krief et al.   PLoS Pathogens

Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA

(2009) P-.H. Fabre et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rosid radiation and the rapid rise of angiosperm-dominated forests

(2009) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"

(2009) V. Hampl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Joining forces in the quest for orthologs

(2009) Toni Gabaldón et al.   GENOME BIOLOGY

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Multigene Phylogeny of Choanozoa and the Origin of Animals

(2008) Kamran Shalchian-Tabrizi et al.   PLoS One