Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees

Van D. Nguyen, Thanh H. Nguyen, Abu Saleh Md Tayeen, H. Dail Laughinghouse, Luna L. Sánchez-Reyes, Jodie Wiggins, Enrico Pontelli, Dmitry Mozzherin, Brian O’Meara, Arlin Stoltzfus

Research output: Contribution to journalArticlepeer-review

Abstract

A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts, including research, education, and public policy. Yet, accessing the tree of life typically requires special knowledge, complex software, or long periods of training. The Phylotastic project aims make it as easy to get a phylogeny of species as it is to get driving directions from mapping software. In prior work, we presented a design for an open system to validate and manage taxon names, find phylogeny resources, extract subtrees matching a user’s taxon list, scale trees to time, and integrate related resources such as species images. Here, we report the implementation of a set of tools that together represent a robust, accessible system for on-the-fly delivery of phylogenetic knowledge. This set of tools includes a web portal to execute several customizable workflows to obtain species phylogenies (scaled by geologic time and decorated with thumbnail images); more than 30 underlying web services (accessible via a common registry); and code toolkits in R and Python (allowing others to develop custom applications using Phylotastic services). The Phylotastic system, accessible via http://www.phylotastic.org, provides a unique resource to access the current state of phylogenetic knowledge, useful for a variety of cases in which a tree extracted quickly from online resources (as distinct from a tree custom-made from character data) is sufficient, as it is for many casual uses of trees identified here.

Original languageEnglish (US)
JournalEvolutionary Bioinformatics
Volume16
DOIs
StatePublished - 2020

Keywords

  • Phylogeny
  • tree of life
  • web services

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Computer Science Applications

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