Rumbling Orchids: How To Assess Divergent Evolution Between Chloroplast Endosymbionts and the Nuclear Host

Genomic perspectives on the birth and spread of plastids: Fig. 1.

(2015) John M. Archibald   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Exploring new dating approaches for parasites: The worldwide Apodanthaceae (Cucurbitales) as an example

(2014) Sidonie Bellot et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular phylogenetics of Neotropical Cyanaeorchis (Cymbidieae, Epidendroideae, Orchidaceae): geographical rather than morphological similarities plus a new species

(2014) Joao Aguiar Nogueira Batista et al.   Phytotaxa

Reconciliation of Gene and Species Trees

(2014) L. Y. Rusin et al.   Biomed Research International

Parasitic plants have increased rates of molecular evolution across all three genomes

(2013) Lindell Bromham et al.   BMC EVOLUTIONARY BIOLOGY

From capsules to nutlets-phylogenetic relationships in the Boraginales

(2013) Maximilian Weigend et al.   CLADISTICS

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

PACo: A Novel Procrustes Application to Cophylogenetic Analysis

(2013) Juan Antonio Balbuena et al.   PLoS One

Phylo-MCOA: A Fast and Efficient Method to Detect Outlier Genes and Species in Phylogenomics Using Multiple Co-inertia Analysis

(2012) D. M. de Vienne et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Horizontal transfer of chloroplast genomes between plant species

(2012) S. Stegemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

A 10-gene phylogeny of Solanum section Herpystichum (Solanaceae) and a comparison of phylogenetic methods

(2011) Eric J. Tepe et al.   AMERICAN JOURNAL OF BOTANY

Energetics and genetics across the prokaryote-eukaryote divide

(2011) Nick Lane   Biology Direct

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

(2011) Botond Sipos et al.   BMC BIOINFORMATICS

Quantifying the Phylodynamic Forces Driving Papillomavirus Evolution

(2011) M. Gottschling et al.   MOLECULAR BIOLOGY AND EVOLUTION

Euclidean Nature of Phylogenetic Distance Matrices

(2011) Damien M. de Vienne et al.   SYSTEMATIC BIOLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

(2010) Bastian Schäferhoff et al.   BMC EVOLUTIONARY BIOLOGY

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Intra-individual polymorphism in diploid and apomictic polyploid hawkweeds (Hieracium, Lactuceae, Asteraceae): disentangling phylogenetic signal, reticulation, and noise

(2009) Judith Fehrer et al.   BMC EVOLUTIONARY BIOLOGY

On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem

(2009) Ran Libeskind-Hadas et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

(2009) O. Akerborg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Molecular Phylogeny of the Neotropical Genus Christensonella (Orchidaceae, Maxillariinae): Species Delimitation and Insights into Chromosome Evolution

(2008) Samantha Koehler et al.   ANNALS OF BOTANY

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

(2008) Kazutaka Katoh et al.   BMC BIOINFORMATICS

Dealing with incongruence in the quest for the species tree: A case study from the orchid genus Satyrium

(2007) Timotheüs van der Niet et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION