FUSTr: a tool to find gene families under selection in transcriptomes
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2018-01-17
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Authors
Cole, T. Jeffrey
Brewer, Michael S.
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Abstract
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.
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DOI
10.7717/peerj.4234