Phylogenomic analysis of Tachinidae (Diptera: Calyptratae: Oestroidea): a transcriptomic approach to understanding the subfamily relationships

Phylogenetic analysis of the tribe Dufouriini (Diptera: Tachinidae) using a total evidence approach based on adult and immature stages

(2022) Marcelo Domingos de Santis et al.   Arthropod Systematics & Phylogeny

Extraordinary diversification of the “bristle flies” (Diptera: Tachinidae) and its underlying causes

(2021) John O Stireman et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein‐encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera: Calyptratae)

(2020) Eliana Buenaventura et al.   SYSTEMATIC ENTOMOLOGY

A phylotranscriptomic framework for flesh fly evolution (Diptera, Calyptratae, Sarcophagidae)

(2020) Liping Yan et al.   CLADISTICS

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

(2019) Sujatha Narayanan Kutty et al.   CLADISTICS

Morphological phylogeny and classification of Winthemiini (Diptera: Tachinidae: Exoristinae)

(2019) André C. Lopes et al.   SYSTEMATIC ENTOMOLOGY

Reclustering the cluster flies (Diptera: Oestroidea, Polleniidae)

(2019) Pierfilippo Cerretti et al.   SYSTEMATIC ENTOMOLOGY

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

Combining transcriptomes and ultraconserved elements to illuminate the phylogeny of Apidae

(2018) Silas Bossert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

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

(2017) Pierfilippo Cerretti et al.   PLoS One

Genomic and transcriptomic resources for assassin flies including the complete genome sequence ofProctacanthus coquilletti(Insecta: Diptera: Asilidae) and 16 representative transcriptomes

(2017) Rebecca B. Dikow et al.   PeerJ

Transcriptomes of three species of Tipuloidea (Diptera, Tipulomorpha) and implications for phylogeny of Tipulomorpha

(2017) Zehui Kang et al.   PLoS One

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

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

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

(2016) Robert Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Review of the New World genus Cholomyia (Diptera, Tachinidae), with a new species from Costa Rica

(2016) Marcelo Domingos de Santis et al.   REVISTA BRASILEIRA DE ENTOMOLOGIA

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

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

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

YBYRÁ facilitates comparison of large phylogenetic trees

(2015) Denis Jacob Machado   BMC BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data

(2014) Ralph S Peters et al.   BMC EVOLUTIONARY BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

(2014) Evgenia V. Kriventseva et al.   NUCLEIC ACIDS RESEARCH

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

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

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Transcriptome Sequences Resolve Deep Relationships of the Grape Family

(2013) Jun Wen et al.   PLoS One

History of tachinid classification (Diptera, Tachinidae)

(2013) James O Hara   ZooKeys

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

(2012) Leigh A. Nelson et al.   GENE

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

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

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

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

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

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

Credit where credit is due: The Goodman–Bremer support metric

(2008) Taran Grant et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION