Evolutionary history of LTR-retrotransposons among 20 Drosophila species

Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

(2016) Camille Sessegolo et al.   Biology Letters

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes

(2016) Nuria Rius et al.   BMC GENOMICS

Do larger genomes contain more diverse transposable elements?

(2015) Tyler A Elliott et al.   BMC EVOLUTIONARY BIOLOGY

VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to theMarinerFamily withinDrosophila

(2015) Gabriel Luz Wallau et al.   MOLECULAR BIOLOGY AND EVOLUTION

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

(2015) Tyler A. Elliott et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus

(2014) Gabriel Wallau et al.   BMC GENOMICS

A New Genome-Wide Method to Track Horizontally Transferred Sequences: Application to Drosophila

(2014) Laurent Modolo et al.   Genome Biology and Evolution

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

(2014) Marc Bailly-Bechet et al.   Mobile DNA

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

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

Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters

(2013) V. Zanni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

tirant, a Newly Discovered Active Endogenous Retrovirus in Drosophila simulans

(2012) A. Akkouche et al.   JOURNAL OF VIROLOGY

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

BEL/Pao retrotransposons in metazoan genomes

(2011) Nicole de la Chaux et al.   BMC EVOLUTIONARY BIOLOGY

The copia retrotransposon and horizontal transfer in Drosophila willistoni

(2011) P. M. RUBIN et al.   Genetics Research

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes

(2010) Emmanuelle Lerat et al.   GENE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution

(2010) Sarah Schaack et al.   TRENDS IN ECOLOGY & EVOLUTION

A triptych of the evolution of plant transposable elements

(2010) Maud I. Tenaillon et al.   TRENDS IN PLANT SCIENCE

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

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

Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

(2009) Carlos Llorens et al.   Biology Direct

Multiple invasions of Gypsy and Micropia retroelements in genus Zaprionus and melanogaster subgroup of the genus Drosophila

(2009) Nathalia de Setta et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes

(2009) Nicole de la Chaux et al.   BMC EVOLUTIONARY BIOLOGY

Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

(2009) E Lerat   HEREDITY

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes

(2009) Carolina Bartolomé et al.   GENOME BIOLOGY

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Revisiting horizontal transfer of transposable elements in Drosophila

(2008) E L S Loreto et al.   HEREDITY

Multiple invasions of Errantivirus in the genus Drosophila

(2008) A. Ludwig et al.   INSECT MOLECULAR BIOLOGY

Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes

(2008) Hsiao-Pei Yang et al.   GENOME BIOLOGY