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

ETE: a python Environment for Tree Exploration

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

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models

(2010) Mukul S Bansal et al.   BMC BIOINFORMATICS

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

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

An algebraic metric for phylogenetic trees

(2009) Ricardo Alberich et al.   APPLIED MATHEMATICS LETTERS

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

(2009) Philippe Gouret et al.   BMC BIOINFORMATICS

A fungal phylogeny based on 82 complete genomes using the composition vector method

(2009) Hao Wang et al.   BMC EVOLUTIONARY BIOLOGY

The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

(2009) Marina Marcet-Houben et al.   PLoS One

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

(2009) Jonathan L. Gordon et al.   PLoS Genetics

A practical method for exact computation of subtree prune and regraft distance

(2008) Y. Wu   BIOINFORMATICS

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

(2008) A. Wehe et al.   BIOINFORMATICS