SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing

(2013) Ali Al-Shahib et al.   BMC BIOINFORMATICS

GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis

(2013) U. Seren et al.   PLANT CELL

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

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

(2012) Pablo Cingolani et al.   FLY

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

(2012) Vincent Segura et al.   NATURE GENETICS

Matapax: An Online High-Throughput Genome-Wide Association Study Pipeline

(2012) L. H. Childs et al.   PLANT PHYSIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects

(2011) Alexis Dereeper et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH