Transposon fingerprinting using low coverage whole genome shotgun sequencing in Cacao (Theobroma cacao L.) and related species

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

(2012) Nolan Kane et al.   AMERICAN JOURNAL OF BOTANY

Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians

(2011) Maud I. Tenaillon et al.   Genome Biology and Evolution

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

(2011) Cheng Sun et al.   Genome Biology and Evolution

Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data

(2011) François Sabot et al.   PLANT JOURNAL

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing

(2010) Eva Hřibová et al.   BMC PLANT BIOLOGY

The Evolution and Diversity of DNA Transposons in the Genome of the Lizard Anolis carolinensis

(2010) Peter A. Novick et al.   Genome Biology and Evolution

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A transposon-induced epigenetic change leads to sex determination in melon

(2009) Antoine Martin et al.   NATURE

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

(2008) Thomas Wicker et al.   BMC GENOMICS

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice

(2008) X. Huang et al.   PLANT PHYSIOLOGY

Geographic and Genetic Population Differentiation of the Amazonian Chocolate Tree (Theobroma cacao L)

(2008) Juan C. Motamayor et al.   PLoS One