Evopipes.net: Bioinformatic tools for ecological and evolutionary genomics

Michael S. Barker, Katrina M. Dlugosch, Louie Dinh, R. Sashikiran Challa, Nolan C. Kane, Matthew G. King, Loren H. Rieseberg

Research output: Contribution to journalArticle

52 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)143-149
Number of pages7
JournalEvolutionary Bioinformatics
Volume2010
Issue number6
DOIs
StatePublished - 2010

Keywords

  • Bioinformatics
  • Ecological genomics
  • Evolutionary genomics
  • Genomic analyses
  • Next-generation sequencing

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Computer Science Applications

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    Barker, M. S., Dlugosch, K. M., Dinh, L., Sashikiran Challa, R., Kane, N. C., King, M. G., & Rieseberg, L. H. (2010). Evopipes.net: Bioinformatic tools for ecological and evolutionary genomics. Evolutionary Bioinformatics, 2010(6), 143-149. https://doi.org/10.4137/EBO.S5861