Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif‐based sequence alignment amid low genetic distances

Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae

(2020) Rong Zhang et al.   SYSTEMATIC BIOLOGY

Conflicting phylogenetic signals in genomic data of the coffee family (Rubiaceae)

(2020) Niklas Wikström et al.   Journal of Systematics and Evolution

Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)

(2020) Verônica A. Thode et al.   Journal of Systematics and Evolution

Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae

(2020) Sidonie Bellot et al.   Scientific Reports

Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species

(2020) Piotr Androsiuk et al.   Scientific Reports

Under the rug: Abandoning persistent misconceptions that obfuscate organelle evolution

(2020) Deise J.P. Gonçalves et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Plastid phylogenomic insights into the evolution of Caryophyllales

(2019) Gang Yao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes

(2019) Deise J.P. Gonçalves et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

(2019) Stephan Greiner et al.   NUCLEIC ACIDS RESEARCH

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments

(2019) Raja Hashim Ali et al.   MOLECULAR BIOLOGY AND EVOLUTION

Role of brassinosteroids in rice spikelet differentiation and degeneration under soil-drying during panicle development

(2019) Weiyang Zhang et al.   BMC PLANT BIOLOGY

Why the monophyly of Nymphaeaceae currently remains indeterminate: an assessment based on gene-wise plastid phylogenomics

(2019) Michael Gruenstaeudl   PLANT SYSTEMATICS AND EVOLUTION

Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics

(2019) Andrew Wanyoike Gichira et al.   Botanical Studies

Characterizing gene tree conflict in plastome-inferred phylogenies

(2019) Joseph F. Walker et al.   PeerJ

The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life

(2019) Yan Du et al.   BMC EVOLUTIONARY BIOLOGY

Insights into the Evolutionary History of the Hawaiian Bidens (Asteraceae) Adaptive Radiation Revealed Through Phylogenomics

(2019) Matthew L Knope et al.   JOURNAL OF HEREDITY

Multi-locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

(2018) David S. Gernandt et al.   AMERICAN JOURNAL OF BOTANY

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Phylogenomic Analysis of the Explosive Adaptive Radiation of the Espeletia Complex (Asteraceae) in the Tropical Andes

(2018) Charles Pouchon et al.   SYSTEMATIC BIOLOGY

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Identification of Ligularia Herbs Using the Complete Chloroplast Genome as a Super-Barcode

(2018) Xinlian Chen et al.   Frontiers in Pharmacology

Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots

(2018) Thomas J. Givnish et al.   AMERICAN JOURNAL OF BOTANY

DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

(2017) Julio Rozas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

(2017) Shu-Dong Zhang et al.   NEW PHYTOLOGIST

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium )

(2017) Oscar M. Vargas et al.   NEW PHYTOLOGIST

Plastome Rearrangements in the “Adenocalymma-Neojobertia” Clade (Bignonieae, Bignoniaceae) and Its Phylogenetic Implications

(2017) Luiz H. M. Fonseca et al.   Frontiers in Plant Science

SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads

(2016) Ruoyan Chen et al.   BIOINFORMATICS

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A new combination in Roldana (Compositae, Senecioneae)

(2016) JOEL CALVO   Phytotaxa

Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline

(2015) Freek T. Bakker et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Plastid phylogenomics and molecular evolution of Alismatales

(2015) T. Gregory Ross et al.   CLADISTICS

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes

(2015) David Roy Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

Is Sequence Alignment an Art or a Science?

(2015) David A. Morrison   SYSTEMATIC BOTANY

Why are most organelle genomes transmitted maternally?

(2014) Stephan Greiner et al.   BIOESSAYS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods

(2014) Muhammad Tariq Pervez et al.   Evolutionary Bioinformatics

Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and Other Angiosperms for Marker Choice

(2014) Nadja Korotkova et al.   PLoS One

Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

(2014) Peng-Fei Ma et al.   SYSTEMATIC BIOLOGY

Influence of Patch Factors and Connectivity on the Avifauna of FragmentedPolylepisForest in the Ecuadorian Andes

(2013) Boris A. Tinoco et al.   BIOTROPICA

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetics of early branching eudicots: Comparing phylogenetic signal across plastid introns, spacers, and genes

(2012) Anna-Magdalena BARNISKE et al.   Journal of Systematics and Evolution

What does it take to resolve relationships and to identify species with molecular markers? An example from the epiphytic Rhipsalideae (Cactaceae)

(2011) Nadja Korotkova et al.   AMERICAN JOURNAL OF BOTANY

The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

(2011) L. Doorduin et al.   DNA RESEARCH

Patterns and causes of incongruence between plastid and nuclear Senecioneae (Asteraceae) phylogenies

(2010) Pieter B. Pelser et al.   AMERICAN JOURNAL OF BOTANY

Correction

(2010) Simon Joly et al.   AMERICAN NATURALIST

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

The deterministic effects of alignment bias in phylogenetic inference

(2010) Mark P. Simmons et al.   CLADISTICS

Alignment of, and phylogenetic inference from, random sequences: The susceptibility of alternative alignment methods to creating artifactual resolution and support

(2010) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Recombination and the maintenance of plant organelle genome stability

(2010) Alexandre Maréchal et al.   NEW PHYTOLOGIST

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

(2010) M. J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trans-splicing of organelle introns - a detour to continuous RNAs

(2009) Stephanie Glanz et al.   BIOESSAYS

Unparalleled GC content in the plastid DNA of Selaginella

(2009) David Roy Smith   PLANT MOLECULAR BIOLOGY

Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA

(2009) Thomas Borsch et al.   PLANT SYSTEMATICS AND EVOLUTION

Taxonomic Revision of Roldana (Asteraceae: Senecioneae), a Genus of the Southwestern U.S.A., Mexico, and Central America1

(2008) A. Michele Funston   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Homology in coding and non-coding DNA sequences: a parsimony perspective

(2008) Helga Ochoterena   PLANT SYSTEMATICS AND EVOLUTION

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY