Phylogenomic analysis of Calyptratae: resolving the phylogenetic relationships within a major radiation of Diptera

Molecular phylogenetics and piercer evolution in the bug-killing flies (Diptera: Tachinidae: Phasiinae)

(2018) JEREMY D. BLASCHKE et al.   SYSTEMATIC ENTOMOLOGY

New data, same story: phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae)

(2018) THOMAS PAULI et al.   SYSTEMATIC ENTOMOLOGY

A phylogenomic analysis of Culicomorpha (Diptera) resolves the relationships among the eight constituent families

(2018) SUJATHA NARAYANAN  KUTTY et al.   SYSTEMATIC ENTOMOLOGY

“Maximum support” = 100% BS

(2018) Andrew V. Z. Brower   CLADISTICS

DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution

(2017) Xuhua Xia   JOURNAL OF HEREDITY

Multilocus and multiregional phylogeny reconstruction of the genus Sarcophaga (Diptera, Sarcophagidae)

(2017) Eliana Buenaventura et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Molecular phylogeny of Miltogramminae (Diptera: Sarcophagidae): Implications for classification, systematics and evolution of larval feeding strategies

(2017) Marcin Piwczyński et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences

(2017) Pierfilippo Cerretti et al.   PLoS One

Ulurumyiidae - a new family of calyptrate flies (Diptera)

(2017) Verner Michelsen et al.   SYSTEMATIC ENTOMOLOGY

Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae)

(2016) Andrew Donovan Young et al.   BMC EVOLUTIONARY BIOLOGY

The first phylogenetic study of Mesembrinellidae (Diptera: Oestroidea) based on molecular data: clades and congruence with morphological characters

(2016) Marco Antonio Tonus Marinho et al.   CLADISTICS

Molecular phylogeny of the hyperdiverse genusSarcophaga(Diptera: Sarcophagidae), and comparison between algorithms for identification of rogue taxa

(2016) Eliana Buenaventura et al.   CLADISTICS

TNT version 1.5, including a full implementation of phylogenetic morphometrics

(2016) Pablo A. Goloboff et al.   CLADISTICS

Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)

(2016) Dong Zhang et al.   International Journal of Biological Sciences

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

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

Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity

(2016) Ana Carolina M. Junqueira et al.   Scientific Reports

Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution

(2016) David K Yeates et al.   Current Opinion in Insect Science

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Say goodbye to tribes in the new house fly classification: A new molecular phylogenetic analysis and an updated biogeographical narrative for the Muscidae (Diptera)

(2015) Kirstern L.F. Haseyama et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae)

(2015) Isaac S. Winkler et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Phylogeny and Evolutionary Timescale of Muscoidea (Diptera: Brachycera: Calyptratae) Inferred from Mitochondrial Genomes

(2015) Shuangmei Ding et al.   PLoS One

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie 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

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Resolves a Spider Backbone Phylogeny and Rejects a Prevailing Paradigm for Orb Web Evolution

(2014) Jason E. Bond et al.   CURRENT BIOLOGY

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

(2014) Patrick Kück et al.   Frontiers in Zoology

Complete tribal sampling reveals basal split in Muscidae (Diptera), confirms saprophagy as ancestral feeding mode, and reveals an evolutionary correlation between instar numbers and carnivory

(2014) Sujatha Narayanan Kutty et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Signal through the noise? Phylogeny of the Tachinidae (Diptera) as inferred from morphological evidence

(2014) PIERFILIPPO CERRETTI et al.   SYSTEMATIC ENTOMOLOGY

Remarkable Rhinophoridae in a growing generic genealogy (Diptera: Calyptratae, Oestroidea)

(2014) PIERFILIPPO CERRETTI et al.   SYSTEMATIC ENTOMOLOGY

Selecting informative subsets of sparse supermatrices increases the chance to find correct trees

(2013) Bernhard Misof et al.   BMC BIOINFORMATICS

Phylogenomics Resolves Evolutionary Relationships among Ants, Bees, and Wasps

(2013) Brian R. Johnson et al.   CURRENT BIOLOGY

Molecular Systematics of the Calliphoridae (Diptera: Oestroidea): Evidence From One Mitochondrial and Three Nuclear Genes

(2013) Baneshwar Singh et al.   JOURNAL OF MEDICAL ENTOMOLOGY

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

(2013) Emiliano Dell’Ampio et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Does better taxon sampling help? A new phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha) based on 50 new taxa and the same old mitochondrial and nuclear markers

(2013) Lei Zhao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reassessment of Paleotachina Townsend and Electrotachina Townsend and their removal from the Tachinidae (Diptera)

(2013) Christopher Raper et al.   ZooKeys

A phylogenetic analysis of Sciomyzidae (Diptera) and some related genera

(2012) Andrea Tóthová et al.   CLADISTICS

Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)

(2012) Leigh A. Nelson et al.   GENE

Molecular phylogenetics of Oestroidea (Diptera: Calyptratae) with emphasis on Calliphoridae: Insights into the inter-familial relationships and additional evidence for paraphyly among blowflies

(2012) M.A.T. Marinho et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The phylogenetic relationships among infraorders and superfamilies of Diptera based on morphological evidence

(2012) CHRISTINE L. LAMBKIN et al.   SYSTEMATIC ENTOMOLOGY

Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria

(2011) Apurva Narechania et al.   Genome Biology and Evolution

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

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

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011

(2010) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly

(2010) SUJATHA NARAYANAN KUTTY et al.   SYSTEMATIC ENTOMOLOGY

On wings of lace: phylogeny and Bayesian divergence time estimates of Neuropterida (Insecta) based on morphological and molecular data

(2010) SHAUN L. WINTERTON et al.   SYSTEMATIC ENTOMOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

Molecular phylogeny of the subfamily Exoristinae (Diptera, Tachinidae), with discussions on the evolutionary history of female oviposition strategy

(2009) TAKUJI TACHI et al.   SYSTEMATIC ENTOMOLOGY

Morphology versus molecules: the phylogenetic relationships of Sepsidae (Diptera: Cyclorrhapha) based on morphology and DNA sequence data from ten genes

(2008) Kathy Feng-Yi Su et al.   CLADISTICS

A phylogeny of the family Fanniidae Schnabl (Insecta�:�Diptera�:�Calyptratae) based on adult morphological characters, with special reference to the Austral species of the genusFannia

(2008) M. C. Domínguez et al.   INVERTEBRATE SYSTEMATICS

Molecular Evolution and Phylogenetic Utility of the Internal Transcribed Spacer 2 (ITS2) in Calyptratae (Diptera: Brachycera)

(2008) Zhong-kui Song et al.   JOURNAL OF MOLECULAR EVOLUTION

The Muscoidea (Diptera: Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes

(2008) Sujatha Narayanan Kutty et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION