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

Deciphering Genome Content and Evolutionary Relationships of Isolates from the FungusMagnaporthe oryzaeAttacking Different Host Plants

(2015) Hélène Chiapello et al.   Genome Biology and Evolution

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

ReproPhylo: An Environment for Reproducible Phylogenomics

(2015) Amir Szitenberg et al.   PLoS Computational Biology

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

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

(2014) E. D. Jarvis et al.   SCIENCE

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

GenBank

(2013) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

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

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

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

(2012) Eric Talevich et al.   BMC BIOINFORMATICS

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

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

BIO::Phylo-phyloinformatic analysis using perl

(2011) Rutger A Vos et al.   BMC BIOINFORMATICS

Rooting the Eukaryotic Tree with Mitochondrial and Bacterial Proteins

(2011) R. Derelle 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

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

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

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

(2010)   PLOS BIOLOGY