Review Paper: The Shape of Phylogenetic Treespace

Characterizing Local Optima for Maximum Parsimony

(2016) Ellen Urheim et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Polyhedral computational geometry for averaging metric phylogenetic trees

(2015) Ezra Miller et al.   ADVANCES IN APPLIED MATHEMATICS

Quantifying MCMC Exploration of Phylogenetic Tree Space

(2015) Chris Whidden et al.   SYSTEMATIC BIOLOGY

Impacts of Terraces on Phylogenetic Inference

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

Point estimates in phylogenetic reconstructions

(2014) P. Benner et al.   BIOINFORMATICS

An Algorithm for Constructing Principal Geodesics in Phylogenetic Treespace

(2014) Tom M. W. Nye   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Towards Improving Searches for Optimal Phylogenies

(2014) Eric Ford et al.   SYSTEMATIC BIOLOGY

On the Neighborhoods of Trees

(2013) Peter J. Humphries et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees

(2012) John Chakerian et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Principal components analysis in the space of phylogenetic trees

(2011) Tom M. W. Nye   ANNALS OF STATISTICS

On agreement forests

(2011) Yang Ding et al.   JOURNAL OF COMBINATORIAL THEORY SERIES A

Terraces in Phylogenetic Tree Space

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

Characterizing the Phylogenetic Tree-Search Problem

(2011) Daniel Money et al.   SYSTEMATIC BIOLOGY

A Fast Algorithm for Computing Geodesic Distances in Tree Space

(2010) Megan Owen et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples

(2009) Michael DeGiorgio et al.   MOLECULAR BIOLOGY AND EVOLUTION

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

Progressive Tree Neighborhood applied to the Maximum Parsimony Problem

(2008) A. Goeffon et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A regular decomposition of the edge-product space of phylogenetic trees

(2007) Jonna Gill et al.   ADVANCES IN APPLIED MATHEMATICS