FUSTr: a tool to find gene families under selection in transcriptomes

PeerJ

T. Jeffrey Cole¹  Michael S. Brewer¹ 

[1]Department of Biology, East Carolina University, Greenville, NC, United States of America

关键词: Transcriptomics;    Positive selection;    Molecular evolution;    Gene family reconstruction;   

DOI  :  10.7717/peerj.4234

来源: DOAJ

【 摘 要 】

Background The recent proliferation of large amounts of biodiversity transcriptomic data has resulted in an ever-expanding need for scalable and user-friendly tools capable of answering large scale molecular evolution questions. FUSTr identifies gene families involved in the process of adaptation. This is a tool that finds genes in transcriptomic datasets under strong positive selection that automatically detects isoform designation patterns in transcriptome assemblies to maximize phylogenetic independence in downstream analysis. Results When applied to previously studied spider transcriptomic data as well as simulated data, FUSTr successfully grouped coding sequences into proper gene families as well as correctly identified those under strong positive selection in relatively little time. Conclusions FUSTr provides a useful tool for novice bioinformaticians to characterize the molecular evolution of organisms throughout the tree of life using large transcriptomic biodiversity datasets and can utilize multi-processor high-performance computational facilities.

【 授权许可】

Unknown