Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference

(2015) Olga Chernomor et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Impacts of Terraces on Phylogenetic Inference

(2015) Michael J. Sanderson et al.   SYSTEMATIC BIOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

The Phylogenetic Likelihood Library

(2014) T. Flouri et al.   SYSTEMATIC BIOLOGY

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

(2013) Emiliano Dell’Ampio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

(2012) Katrin Nyakatura et al.   BMC BIOLOGY

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

(2012) Mark S. Springer et al.   PLoS One

Using Supermatrices for Phylogenetic Inquiry: An Example Using the Sedges

(2012) Cody E. Hinchliff et al.   SYSTEMATIC BIOLOGY

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

(2011) Anne Kupczok et al.   Algorithms for Molecular Biology

Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees

(2011) Fernando Izquierdo-Carrasco et al.   BMC BIOINFORMATICS

Statistics and Truth in Phylogenomics

(2011) S. Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Terraces in Phylogenetic Tree Space

(2011) M. J. Sanderson et al.   SCIENCE

Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data

(2010) A. Stamatakis et al.   BIOINFORMATICS

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics

(2010) Raphaël Helaers et al.   BMC BIOINFORMATICS

A supermatrix-based molecular phylogeny of the family Drosophilidae

(2010) KIM VAN DER LINDE et al.   Genetics Research

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees

(2010) R. Alexander Pyron et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling

(2008) Yanis Bouchenak-Khelladi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

(2008) A. Stamatakis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES