title: EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.
abstract: Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among the chief problems posed by next-generation sequencing are assembly and analyses of these large data sets. Here we present an online server, http://EvoPipes.net, that provides access to a wide range of tools for bioinformatic analyses of genomic data oriented for ecological and evolutionary biologists. The EvoPipes.net server includes a basic tool kit for analyses of genomic data including a next-generation sequence cleaning pipeline (SnoWhite), scaffolded assembly software (SCARF), a reciprocal best-blast hit ortholog pipeline (RBH Orthologs), a pipeline for reference protein-based translation and identification of reading frame in transcriptome and genomic DNA (TransPipe), a pipeline to identify gene families and summarize the history of gene duplications (DupPipe), and a tool for developing SSRs or microsatellites from a transcriptome or genomic coding sequence collection (findSSR). EvoPipes.net also provides links to other software developed for evolutionary and ecological genomics, including chromEvol and NU-IN, as well as a forum for discussions of issues relating to genomic analyses and interpretation of results. Overall, these applications provide a basic bioinformatic tool kit that will enable ecologists and evolutionary biologists with relatively little experience and computational resources to take advantage of the opportunities provided by next-generation sequencing in their systems.
authors.affiliation: The Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Barker
authors.forename: Katrina M
authors.initials: KM
authors.lastname: Dlugosch
authors.forename: Louie
authors.initials: L
authors.lastname: Dinh
authors.forename: R Sashikiran
authors.initials: RS
authors.lastname: Challa
authors.forename: Nolan C
authors.initials: NC
authors.lastname: Kane
authors.forename: Matthew G
authors.initials: MG
authors.lastname: King
authors.forename: Loren H
authors.initials: LH
authors.lastname: Rieseberg