Iroki: automatic customization and visualization of phylogenetic trees.

PeerJ
Ryan M MooreK. E. Wommack

Abstract

Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki's utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of...Continue Reading

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Citations

Jan 23, 2021·Anaerobe·Tomaž Accetto, Gorazd Avguštin
Feb 10, 2021·G3 : Genes - Genomes - Genetics·Sevgin DemirciSander Peters
Feb 19, 2021·Nature Communications·Peter M HeinemannBernhard Hauer
Feb 23, 2021·PeerJ·Beata Grzywacz, Piotr Skórka
Aug 13, 2021·Frontiers in Human Neuroscience·Alejandro Rodríguez-Collado, Cristina Rueda
Sep 4, 2021·Nucleic Acids Research·Kok Zhi LeeKevin V Solomon

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Methods Mentioned

BETA
PCA

Software Mentioned

QIIME
Evolview
HTML5 Canvas
VIROME
ETE
Phylemon
SVG
runif
LALOLib computing library
Phylo

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