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.

Keywords: bioinformatics; ecological genomics; evolutionary genomics; genomic analyses; next-generation sequencing.

Figure 1.

An outline of data analyses possible with tools available on the http://EvoPipes.net server. Purple diamonds represent sequence data provided by the user, the blue ovals indicate analyses that may be conducted with EvoPipes.net tools, and the gray rectangle represents steps requiring software from other sources. Note that ChromEvol requires chromosome number and phylogenetic information as input rather than sequence data. However, ChromEvol results can be informed by genomic analyses with DupPipe.

Figure 2.

A) The EvoPipes.net home page with icons representing each bioinformatic analysis available on the server. B) Example upload page for the DupPipe. C) Example results download page for the DupPipe.