Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data

(2012) Sabrina Simon et al.   Genome Biology and Evolution

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

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

Advances in Insect Phylogeny at the Dawn of the Postgenomic Era

(2011) Michelle D. Trautwein et al.   Annual Review of Entomology

Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda

(2011) B. M. von Reumont et al.   MOLECULAR BIOLOGY AND EVOLUTION

Can sensitivity analysis help to detect long-branch attraction?

(2011) Samuli Lehtonen   MOLECULAR PHYLOGENETICS AND EVOLUTION

Spurious 99% bootstrap and jackknife support for unsupported clades

(2011) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Sperm accessory microtubules suggest the placement of Diplura as the sister-group of Insecta s.s.

(2010) Romano Dallai et al.   ARTHROPOD STRUCTURE & DEVELOPMENT

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

(2010) Ben C Stöver et al.   BMC BIOINFORMATICS

Phylogenomics with incomplete taxon coverage: the limits to inference

(2010) Michael J Sanderson et al.   BMC EVOLUTIONARY BIOLOGY

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

(2010) Patrick Kück et al.   Frontiers in Zoology

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

(2010) Jerome C. Regier et al.   NATURE

Characterizing phylogenetically decisive taxon coverage

(2009) Mike Steel et al.   APPLIED MATHEMATICS LETTERS

400 million years on six legs: On the origin and early evolution of Hexapoda

(2009) David A. Grimaldi   ARTHROPOD STRUCTURE & DEVELOPMENT

Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships

(2009) Björn M von Reumont et al.   BMC EVOLUTIONARY BIOLOGY

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction

(2009) Jon Mallatt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

(2009) L. Lacey Knowles   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Phylogenetic Relationships of Basal Hexapods Reconstructed from Nearly Complete 18S and 28S rRNA Gene Sequences

(2009) Yan Gao et al.   ZOOLOGICAL SCIENCE

Recent developments in the MAFFT multiple sequence alignment program

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

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence

(2008) Jerome C. Regier et al.   SYSTEMATIC BIOLOGY

Testing for misleading effects in the phylogenetic reconstruction of ancient lineages of hexapods: influence of character dependence and character choice in analyses of 28S rRNA sequences

(2008) Emiliano Dell’Ampio et al.   ZOOLOGICA SCRIPTA