OneTwoTree: An online tool for phylogeny reconstruction

Molecular Ecology Resources
Michal DroriItay Mayrose

Abstract

Phylogeny reconstruction is a key instrument in numerous biological analyses, ranging from evolutionary and ecology research, to conservation and systems biology. The increasing accumulation of genomic data makes it possible to reconstruct phylogenies with both high accuracy and at increasingly finer resolution. Yet, taking advantage of the enormous amount of sequence data available requires the use of computational tools for efficient data retrieval and processing, or else the process could quickly become an error-prone endeavour. Here, we present OneTwoTree (http://onetwotree.tau.ac.il/), a Web-based tool for tree reconstruction based on the supermatrix paradigm. Given a list of taxa names of interest as the sole input requirement, OneTwoTree retrieves all available sequence data from NCBI GenBank, clusters these into orthology groups, identifies the most informative set of markers, searches for an appropriate outgroup, and assembles a partitioned sequence matrix that is then used for the final phylogeny reconstruction step. OneTwoTree further allows users to control various steps of the process, such as the merging of sequences from similar clusters, or phylogeny reconstruction based on markers from a specific genome type. B...Continue Reading

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Citations

May 8, 2019·Molecular Biology and Evolution·Mario A Cerón-RomeroL A Katz
Jul 14, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Jurriaan M de VosKay Lucek
Mar 19, 2020·Ecology and Evolution·Cody Coyotee Howard, Nico Cellinese
Apr 22, 2020·Ecology and Evolution·Martin BitomskýMartin Duchoslav
Jan 31, 2019·Nature Ecology & Evolution·Anna RiceItay Mayrose
Nov 24, 2020·The New Phytologist·Anna Rice, Itay Mayrose
Mar 10, 2021·American Journal of Botany·Cody Coyotee HowardNico Cellinese
Mar 26, 2021·Current Microbiology·Shira Penner, Yuval Sapir

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