title: Galaxy tools to study genome diversity.
abstract: BACKGROUND
  Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for small labs to obtain full-genome variation data from their species of interest. However, those labs may not have easy access to, and familiarity with, computational tools to analyze those data.
  
  
  RESULTS
  We have created a suite of tools for the Galaxy web server aimed at handling nucleotide and amino-acid polymorphisms discovered by full-genome sequencing of several individuals of the same species, or using a SNP genotyping microarray. In addition to providing user-friendly tools, a main goal is to make published analyses reproducible. While most of the examples discussed in this paper deal with nuclear-genome diversity in non-human vertebrates, we also illustrate the application of the tools to fungal genomes, human biomedical data, and mitochondrial sequences.
  
  
  CONCLUSIONS
  This project illustrates that a small group can design, implement, test, document, and distribute a Galaxy tool collection to meet the needs of a particular community of biologists.
authors.forename: Oscar C
authors.initials: OC
authors.lastname: Bedoya-Reina
authors.forename: Aakrosh
authors.initials: A
authors.lastname: Ratan
authors.forename: Richard
authors.initials: R
authors.lastname: Burhans
authors.forename: Hie Lim
authors.initials: HL
authors.lastname: Kim
authors.forename: Belinda
authors.initials: B
authors.lastname: Giardine
authors.forename: Cathy
authors.initials: C
authors.lastname: Riemer
authors.forename: Qunhua
authors.initials: Q
authors.lastname: Li
authors.forename: Thomas L
authors.initials: TL
authors.lastname: Olson
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Loughran
authors.forename: Bridgett M
authors.initials: BM
authors.lastname: Vonholdt
authors.forename: George H
authors.initials: GH
authors.lastname: Perry
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA. webb@bx.psu.edu.
authors.forename: Webb
authors.initials: W
authors.lastname: Miller