4.5 Article

Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data

Related references

Note: Only part of the references are listed.
Article Evolutionary Biology

Chloroplast Phylogenomics Indicates that Ginkgo biloba Is Sister to Cycads

Chung-Shien Wu et al.

GENOME BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny

Todd H. Oakley et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

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

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Review Biochemistry & Molecular Biology

Applications of next-generation sequencing to phylogeography and phylogenetics

John E. McCormack et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2013)

Article Genetics & Heredity

A heterozygous moth genome provides insights into herbivory and detoxification

Minsheng You et al.

NATURE GENETICS (2013)

Article Plant Sciences

TARGETED ENRICHMENT STRATEGIES FOR NEXT-GENERATION PLANT BIOLOGY

Richard Cronn et al.

AMERICAN JOURNAL OF BOTANY (2012)

Review Entomology

Advances in Insect Phylogeny at the Dawn of the Postgenomic Era

Michelle D. Trautwein et al.

ANNUAL REVIEW OF ENTOMOLOGY, VOL 57 (2012)

Article Evolutionary Biology

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

Sabrina Simon et al.

GENOME BIOLOGY AND EVOLUTION (2012)

Article Biochemistry & Molecular Biology

Characterization of the Complete Mitochondrial Genomes of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae)

Huan-Na Chai et al.

INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES (2012)

Article Biochemistry & Molecular Biology

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

Bjoern M. von Reumont et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Biochemistry & Molecular Biology

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

Robert Lanfear et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Article Biochemistry & Molecular Biology

GenBank

Dennis A. Benson et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Multidisciplinary Sciences

A Molecular Phylogeny of Hemiptera Inferred from Mitochondrial Genome Sequences

Nan Song et al.

PLOS ONE (2012)

Article Evolutionary Biology

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

Alan R. Lemmon et al.

SYSTEMATIC BIOLOGY (2012)

Article Evolutionary Biology

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

Brant C. Faircloth et al.

SYSTEMATIC BIOLOGY (2012)

Article Biochemistry & Molecular Biology

The Monarch Butterfly Genome Yields Insights into Long-Distance Migration

Shuai Zhan et al.

Article Biochemistry & Molecular Biology

Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics

Benoit Nabholz et al.

MOLECULAR BIOLOGY AND EVOLUTION (2011)

Article Evolutionary Biology

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

John J. Wiens et al.

SYSTEMATIC BIOLOGY (2011)

Article Biochemical Research Methods

iGTP: A software package for large-scale gene tree parsimony analysis

Ruchi Chaudhary et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Optimization of de novo transcriptome assembly from next-generation sequencing data

Yann Surget-Groba et al.

GENOME RESEARCH (2010)

Article Biochemistry & Molecular Biology

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

Karen Meusemann et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Article Biochemistry & Molecular Biology

Expressed sequence tags reveal Proctotrupomorpha (minus Chalcidoidea) as sister to Aculeata (Hymenoptera: Insecta)

Barbara J. Sharanowski et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2010)

Review Biochemical Research Methods

Target-enrichment strategies for next-generation sequencing

Lira Mamanova et al.

NATURE METHODS (2010)

Article Biochemistry & Molecular Biology

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

Federico Abascal et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

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

Chris Todd Hittinger et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

Nicolas Lartillot et al.

BIOINFORMATICS (2009)

Article Evolutionary Biology

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

Ingo Ebersberger et al.

BMC EVOLUTIONARY BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Removal of Noisy Characters from Chloroplast Genome-Scale Data Suggests Revision of Phylogenetic Placements of Amborella and Ceratophyllum

Vadim V. Goremykin et al.

JOURNAL OF MOLECULAR EVOLUTION (2009)

Review Entomology

Ancient rapid radiations of insects: Challenges for phylogenetic analysis

James B. Whitfield et al.

ANNUAL REVIEW OF ENTOMOLOGY (2008)

Article Evolutionary Biology

TNT, a free program for phylogenetic analysis

Pablo A. Goloboff et al.

CLADISTICS (2008)

Article Developmental Biology

Additional Molecular Support for the New Chordate Phylogeny

Frederic Delsuc et al.

GENESIS (2008)

Article Biochemical Research Methods

RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Alexandros Stamatakis

BIOINFORMATICS (2006)

Article Biochemical Research Methods

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Weizhong Li et al.

BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles)

J Hughes et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Biochemistry & Molecular Biology

A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region

SM Chaw et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2005)

Article Biochemistry & Molecular Biology

MAFFT version 5: improvement in accuracy of multiple sequence alignment

K Katoh et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Multidisciplinary Sciences

A draft sequence for the genome of the domesticated silkworm (Bombyx mori)

QY Xia et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

N Lartillot et al.

MOLECULAR BIOLOGY AND EVOLUTION (2004)

Article Evolutionary Biology

Missing data, incomplete taxa, and phylogenetic accuracy

JJ Wiens

SYSTEMATIC BIOLOGY (2003)

Article Biochemistry & Molecular Biology

An index of substitution saturation and its application

XH Xia et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2003)

Article Multidisciplinary Sciences

Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils

PS Soltis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)