STRIDE: Species Tree Root Inference from Gene Duplication Events

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

(2016) Elisabeth Veeckman et al.   PLANT CELL

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

New substitution models for rooting phylogenetic trees

(2015) Tom A. Williams et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

(2014) M. dos Reis et al.   Biology Letters

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) E. D. Jarvis et al.   SCIENCE

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective

(2014) F. Burki   Cold Spring Harbor Perspectives in Biology

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

(2013) Y.-C. Wu et al.   GENOME RESEARCH

Unrooted Tree Reconciliation: A Unified Approach

(2013) Pawel Gorecki et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

DrML: Probabilistic Modeling of Gene Duplications

(2013) Paweł Górecki et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

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

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

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

(2011) L. W. Parfrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

TriTrypDB: a functional genomic resource for the Trypanosomatidae

(2009) Martin Aslett et al.   NUCLEIC ACIDS RESEARCH