Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

(2020) Tobias Andermann et al.   Frontiers in Genetics

SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets

(2020) Daniel M. Portik et al.   Methods in Ecology and Evolution

Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana)

(2020) Kin Onn Chan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci

(2019) Marshal Hedin et al.   PeerJ

Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores)

(2019) Noor D. White et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The performance of coalescent-based species tree estimation methods under models of missing data

(2018) Michael Nute et al.   BMC GENOMICS

Estimating Improved Partitioning Schemes for Ultraconserved Elements

(2018) Victor A Tagliacollo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci

(2018) Jeffrey W. Streicher et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

On the universality of target-enrichment baits for phylogenomic research

(2018) Silas Bossert et al.   Methods in Ecology and Evolution

SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

(2018) Tobias Andermann et al.   PeerJ

Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods

(2018) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

PyPHLAWD: a python tool for phylogenetic dataset construction

(2018) Stephen A. Smith et al.   Methods in Ecology and Evolution

Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

(2017) S.J. Longo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

(2017) Erin K Molloy et al.   SYSTEMATIC BIOLOGY

Phylotranscriptomic consolidation of the jawed vertebrate timetree

(2017) Iker Irisarri et al.   Nature Ecology & Evolution

Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status

(2016) João Filipe Riva Tonini et al.   BIOLOGICAL CONSERVATION

Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?

(2016) Adam D. Leaché et al.   BMC EVOLUTIONARY BIOLOGY

Scaling statistical multiple sequence alignment to large datasets

(2016) Michael Nute et al.   BMC GENOMICS

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

(2016) Daniel M. Portik et al.   Molecular Ecology Resources

Phylogenomic analyses reveal novel relationships among snake families

(2016) Jeffrey W. Streicher et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

(2016) Yuchi Zheng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

(2016) Charles W. Linkem et al.   SYSTEMATIC BIOLOGY

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

A comparative study of SVDquartets and other coalescent-based species tree estimation methods

(2015) Jed Chou et al.   BMC GENOMICS

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

Multiple sequence alignment modeling: methods and applications

(2015) Maria Chatzou et al.   BRIEFINGS IN BIOINFORMATICS

Phylogenomics of Horned Lizards (Genus:Phrynosoma) Using Targeted Sequence Capture Data

(2015) Adam D. Leaché et al.   COPEIA

SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage

(2015) William A. Freyman   Evolutionary Bioinformatics

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

(2015) Siavash Mirarab et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Impact of Missing Data on Species Tree Estimation

(2015) Zhenxiang Xi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

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

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

Ultra-large alignments using phylogeny-aware profiles

(2015) Nam-phuong D. Nguyen et al.   GENOME BIOLOGY

Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

(2015) Tod W. Reeder et al.   PLoS One

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

(2015) Md Shamsuzzoha Bayzid et al.   PLoS One

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

(2013) R Pyron et al.   BMC EVOLUTIONARY BIOLOGY

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

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

phyloGenerator: an automated phylogeny generation tool for ecologists

(2013) William D. Pearse et al.   Methods in Ecology and Evolution

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

(2012) J. J. Wiens et al.   Biology Letters

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Accounting For Alignment Uncertainty in Phylogenomics

(2012) Martin Wu et al.   PLoS One

Who Speaks with a Forked Tongue?

(2012) J. B. Losos et al.   SCIENCE

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

(2011) Ted M. Townsend et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

(2009) Carsten Kemena et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Noisy: Identification of problematic columns in multiple sequence alignments

(2008) Andreas WM Dress et al.   Algorithms for Molecular Biology

Branch Lengths, Support, and Congruence: Testing the Phylogenomic Approach with 20 Nuclear Loci in Snakes

(2008) John J. Wiens et al.   SYSTEMATIC BIOLOGY