Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study

PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics

(2013) Kevin M. Kocot et al.   Evolutionary Bioinformatics

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

A heterozygous moth genome provides insights into herbivory and detoxification

(2013) Minsheng You et al.   NATURE GENETICS

A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

(2013) Jerome C. Regier et al.   PLoS One

A Molecular Phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and Its Implications for Classification, Biogeography and the Evolution of Host Plant Use

(2013) Jae-Cheon Sohn et al.   PLoS One

Characterization of the Complete Mitochondrion Genome of Diurnal Moth Amata emma (Butler) (Lepidoptera: Erebidae) and Its Phylogenetic Implications

(2013) Hui-Fen Lu et al.   PLoS One

Adding unaligned sequences into an existing alignment using MAFFT and LAST

(2012) Kazutaka Katoh et al.   BIOINFORMATICS

High-Throughput Transcriptome Sequencing for Snp and Gene Discovery in a Moth

(2012) Nicholas J. Miller et al.   ENVIRONMENTAL ENTOMOLOGY

A Molecular Phylogeny for the Leaf-Roller Moths (Lepidoptera: Tortricidae) and Its Implications for Classification and Life History Evolution

(2012) Jerome C. Regier et al.   PLoS One

Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing

(2012) Yinü Li et al.   PLoS One

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

(2012) John J. Wiens et al.   PLoS One

Resolving Discrepancy between Nucleotides and Amino Acids in Deep-Level Arthropod Phylogenomics: Differentiating Serine Codons in 21-Amino-Acid Models

(2012) Andreas Zwick et al.   PLoS One

A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification

(2012) JEROME C. REGIER et al.   SYSTEMATIC ENTOMOLOGY

Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae)

(2011) Akito Y Kawahara et al.   BMC EVOLUTIONARY BIOLOGY

The Monarch Butterfly Genome Yields Insights into Long-Distance Migration

(2011) Shuai Zhan et al.   CELL

Phylogeny of the mega-diverse Gelechioidea (Lepidoptera): Adaptations and determinants of success

(2011) Lauri Kaila et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reconstructing intraordinal relationships in Lepidoptera using mitochondrial genome data with the description of two newly sequenced lycaenids, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae)

(2011) Min Jee Kim et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Comprehensive Molecular Sampling Yields a Robust Phylogeny for Geometrid Moths (Lepidoptera: Geometridae)

(2011) Pasi Sihvonen et al.   PLoS One

Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods

(2011) Jerome C. Regier et al.   PLoS One

Episodic radiations in the fly tree of life

(2011) B. M. Wiegmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cretaceous origin and repeated tertiary diversification of the redefined butterflies

(2011) M. Heikkila et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?

(2011) Soowon Cho et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

The Heterobathmia life history elucidated: Immature stages contradict assignment to suborder Zeugloptera (Insecta, Lepidoptera)

(2010) N. P. Kristensen et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

(2010) K. S. Pick et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

(2010) C. T. Hittinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies

(2010) M. Mutanen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study

(2009) Jerome C Regier et al.   BMC EVOLUTIONARY BIOLOGY

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

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology

(2009) Jun Duan et al.   NUCLEIC ACIDS RESEARCH

Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences

(2009) Tae-Kun Seo et al.   SYSTEMATIC BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE