Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae)

Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment

(2015) J. D. Stephens et al.   AMERICAN JOURNAL OF BOTANY

Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture

(2015) Karolina Heyduk et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Re-evaluating the phylogeny of allopolyploid Gossypium L.

(2015) Corrinne E. Grover et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment

(2015) Jessica D. Stephens et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Post-molecular systematics and the future of phylogenetics

(2015) R. Alexander Pyron   TRENDS IN ECOLOGY & EVOLUTION

Using phylogenomics to resolve mega-families: An example from Compositae

(2015) Jennifer R. Mandel et al.   Journal of Systematics and Evolution

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

(2015) James A. Nicholls et al.   Frontiers in Plant Science

MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes

(2015) Srikar Chamala et al.   Applications in Plant Sciences

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Plastid phylogenomics and green plant phylogeny: almost full circle but not quite there

(2014) Charles C Davis et al.   BMC BIOLOGY

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines

(2014) Michael DeGiorgio et al.   BMC EVOLUTIONARY BIOLOGY

Pre-Pleistocene origin of an endangered habitat: links between vernal pools and aquaticOxalisin the Greater Cape Floristic Region of South Africa

(2014) Kenneth C. Oberlander et al.   JOURNAL OF BIOGEOGRAPHY

Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing

(2014) Filipe de Sousa et al.   PLoS One

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

Primers for Low-Copy Nuclear Genes in Metrosideros and Cross-Amplification in Myrtaceae

(2014) Yohan Pillon et al.   Applications in Plant Sciences

A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

(2014) Jennifer R. Mandel et al.   Applications in Plant Sciences

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): A next-generation sequencing transcriptomic approach

(2013) Jeanne Tonnabel et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

STRAW: Species TRee Analysis Web server

(2013) Timothy I. Shaw et al.   NUCLEIC ACIDS RESEARCH

Targeted Enrichment: Maximizing Orthologous Gene Comparisons across Deep Evolutionary Time

(2013) Shannon M. Hedtke et al.   PLoS One

Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns

(2013) Carl J. Rothfels et al.   PLoS One

Decrease of sexual organ reciprocity between heterostylous primrose species, with possible functional and evolutionary implications

(2012) Barbara Keller et al.   ANNALS OF BOTANY

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

(2012) M. Kearse et al.   BIOINFORMATICS

Do we still need supertrees?

(2012) Arndt von Haeseler   BMC BIOLOGY

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

(2012) Matthew Parks et al.   BMC EVOLUTIONARY BIOLOGY

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

Unified modeling of gene duplication, loss, and coalescence using a locus tree

(2012) M. D. Rasmussen et al.   GENOME RESEARCH

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Long identical multispecies elements in plant and animal genomes

(2012) J. Reneker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Diversification of the American bulb-bearing Oxalis (Oxalidaceae): Dispersal to North America and modification of the tristylous breeding system

(2011) Andrew G. Gardner et al.   AMERICAN JOURNAL OF BOTANY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

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

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

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

(2010) Thomas J. Givnish et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plant-pollinator associations

(2009) Julien P Renoult et al.   BMC EVOLUTIONARY BIOLOGY

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

GenomeVx: simple web-based creation of editable circular chromosome maps

(2008) G. C. Conant et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION