Article

 

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics. Público Deposited

https://scholar.colorado.edu/concern/articles/8w32r638m
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.
Creator
Date Issued
  • 2010-10-20
Academic Affiliation
Journal Title
Journal Volume
  • 6
File Extent
  • 143-149
Subject
Última modificación
  • 2019-12-05
Identifier
  • PubMed ID: 21079755
Resource Type
Declaración de derechos
DOI
ISSN
  • 1176-9343
Language
License

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