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phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R

1
Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
2
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden
3
Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
4
Gothenburg Botanical Garden, Carl Skottsbergsgata 22A, SE-413 19 Gothenburg, Sweden
5
Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138 USA
*
Author to whom correspondence should be addressed.
Received: 28 March 2018 / Revised: 26 May 2018 / Accepted: 1 June 2018 / Published: 5 June 2018
(This article belongs to the Special Issue Open Science Phyloinformatics: Resources, Methods, and Analyses)
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Abstract

The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabeling encountered when searching for suitable sequences for phylogenetic analysis. These issues include, among others, the incorrect identification of sequenced species, non-standardized and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inference, a risk that is likely to increase with the size of phylogenies or the molecular datasets used to generate them. Here we present a software package, phylotaR that bypasses the above issues by using instead an alignment search tool to identify orthologous sequences. Our package builds on the framework of its predecessor, PhyLoTa, by providing a modular pipeline for identifying overlapping sequence clusters using up-to-date GenBank data and providing new features, improvements and tools. We demonstrate and test our pipeline’s effectiveness by presenting trees generated from phylotaR clusters for two large taxonomic clades: Palms and primates. Given the versatility of this package, we hope that it will become a standard tool for any research aiming to use GenBank data for phylogenetic analysis. View Full-Text
Keywords: BLAST; DNA; open source; phylogenetics; R; sequence orthology BLAST; DNA; open source; phylogenetics; R; sequence orthology
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Bennett, D.J.; Hettling, H.; Silvestro, D.; Zizka, A.; Bacon, C.D.; Faurby, S.; Vos, R.A.; Antonelli, A. phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R. Life 2018, 8, 20.

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