Iroki: automatic customization and visualization of phylogenetic trees
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 evolutiona...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2020-02-01
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| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/8584.pdf |
| _version_ | 1797420321831124992 |
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| author | Ryan M. Moore Amelia O. Harrison Sean M. McAllister Shawn W. Polson K. Eric Wommack |
| author_facet | Ryan M. Moore Amelia O. Harrison Sean M. McAllister Shawn W. Polson K. Eric Wommack |
| author_sort | Ryan M. Moore |
| collection | DOAJ |
| description | 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 metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki. |
| first_indexed | 2024-03-09T06:59:51Z |
| format | Article |
| id | doaj.art-2e7de47bb9fe4674bb6705fc5fdf3eec |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:59:51Z |
| publishDate | 2020-02-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-2e7de47bb9fe4674bb6705fc5fdf3eec2023-12-03T09:54:14ZengPeerJ Inc.PeerJ2167-83592020-02-018e858410.7717/peerj.8584Iroki: automatic customization and visualization of phylogenetic treesRyan M. Moore0Amelia O. Harrison1Sean M. McAllister2Shawn W. Polson3K. Eric Wommack4Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of AmericaSchool of Marine Science and Policy, University of Delaware, Newark, DE, United States of AmericaSchool of Marine Science and Policy, University of Delaware, Newark, DE, United States of AmericaCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of AmericaCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of AmericaPhylogenetic 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 metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.https://peerj.com/articles/8584.pdfBioinformaticsEnvironmental microbiologyPhylogenySequence analysisMetagenomicsMicrobiome |
| spellingShingle | Ryan M. Moore Amelia O. Harrison Sean M. McAllister Shawn W. Polson K. Eric Wommack Iroki: automatic customization and visualization of phylogenetic trees PeerJ Bioinformatics Environmental microbiology Phylogeny Sequence analysis Metagenomics Microbiome |
| title | Iroki: automatic customization and visualization of phylogenetic trees |
| title_full | Iroki: automatic customization and visualization of phylogenetic trees |
| title_fullStr | Iroki: automatic customization and visualization of phylogenetic trees |
| title_full_unstemmed | Iroki: automatic customization and visualization of phylogenetic trees |
| title_short | Iroki: automatic customization and visualization of phylogenetic trees |
| title_sort | iroki automatic customization and visualization of phylogenetic trees |
| topic | Bioinformatics Environmental microbiology Phylogeny Sequence analysis Metagenomics Microbiome |
| url | https://peerj.com/articles/8584.pdf |
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