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

A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

(2017) Timothée Bonnet et al.   EVOLUTION

Pinus vallartensis (Pinaceae), a new species from western Jalisco, Mexico

(2017) JORGE A. PÉREZ DE LA ROSA et al.   Phytotaxa

Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes)

(2017) Xitlali Aguirre-Dugua et al.   Mitochondrial DNA Part B-Resources

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant SpeciesArabidopsis thaliana(L.) Heynh

(2015) Noah W. M. Stenz et al.   SYSTEMATIC BIOLOGY

Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA inAsclepias(Apocynaceae)

(2015) Kevin Weitemier et al.   PeerJ

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

(2014) Diana M. Percy et al.   MOLECULAR ECOLOGY

Disparate parametric branch-support values from ambiguous characters

(2014) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models

(2014) Lam si Tung Ho et al.   SYSTEMATIC BIOLOGY

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

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

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

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

Whole-exome targeted sequencing of the uncharacterized pine genome

(2013) Leandro G. Neves et al.   PLANT JOURNAL

Phylogenetic Relationships and Species Delimitation in Pinus Section Trifoliae Inferrred from Plastid DNA

(2013) Sergio Hernández-León et al.   PLoS One

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

(2012) M. Kearse et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

(2012) Andre J. Aberer et al.   SYSTEMATIC BIOLOGY

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

Effect of natural root grafting on growth response of jack pine (Pinus banksiana ; Pinaceae)

(2011) Emilie Tarroux et al.   AMERICAN JOURNAL OF BOTANY

An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

(2011) Craig S Echt et al.   BMC GENETICS

Phylogeography of Pinus subsection Australes in the Caribbean Basin

(2010) Lev Jardón-Barbolla et al.   ANNALS OF BOTANY

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

(2010) Bret R. Larget et al.   BIOINFORMATICS

Pinus georginae (Pinaceae), a new species from western Jalisco, Mexico

(2010) Jorge Alberto Pérez de la Rosa   BRITTONIA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Reticulate evolution and incomplete lineage sorting among the ponderosa pines

(2009) Ann Willyard et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Species Tree Inference by Minimizing Deep Coalescences

(2009) Cuong Than et al.   PLoS Computational Biology

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Quartets MaxCut: A Divide and Conquer Quartets Algorithm

(2008) Sagi Snir et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Use of Simultaneous Analyses to Guide Fossil‐Based Calibrations of Pinaceae Phylogeny

(2008) David S. Gernandt et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae)

(2008) ASHLEY B. MORRIS et al.   MOLECULAR ECOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY

Identification of COS markers in the Pinaceae

(2008) Cherdsak Liewlaksaneeyanawin et al.   Tree Genetics & Genomes