Article
EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics. Public 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
- Last Modified
- 2019-12-05
- Identifier
- PubMed ID: 21079755
- Resource Type
- Rights Statement
- DOI
- ISSN
- 1176-9343
- Language
- License
Relationships
Items
Thumbnail | Title | Date Uploaded | Visibility | Actions |
---|---|---|---|---|
evopipesNetBioinformaticToolsForEcologicalAndEvolutionary.pdf | 2019-12-05 | Public | Download |