Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

(2014) Naama Menda et al.   BMC PLANT BIOLOGY

Differences in insect resistance between tomato species endemic to the Galapagos Islands

(2013) Alejandro F Lucatti et al.   BMC EVOLUTIONARY BIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

(2013) D. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

(2012) Aureliano Bombarely et al.   BMC GENOMICS

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

(2012) Joanne A Labate et al.   BMC PLANT BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction

(2011) Cécile Ané   Genome Biology and Evolution

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Rate of meristem maturation determines inflorescence architecture in tomato

(2011) S. J. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes

(2011) J. P. Hamilton et al.   Database-The Journal of Biological Databases and Curation

Spatial genetics of wild tomato species reveals roles of the Andean geography on demographic history

(2010) T. Nakazato et al.   AMERICAN JOURNAL OF BOTANY

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

(2010) A. Bombarely et al.   NUCLEIC ACIDS RESEARCH

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

Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection

(2009) Jochen B. W. Wolf et al.   Genome Biology and Evolution

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

A clarified position for solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (solanaceae)

(2008) Nicolas Ranc et al.   BMC PLANT BIOLOGY