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TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata

M. Pirrung, R. Kennedy, J. G. Caporaso, J. Stombaugh, D. Wendel, R. Knight
2011 Bioinformatics  
Results: TopiaryExplorer supports the visualization of very large phylogenetic trees, including features such as the automated coloring of branches by environmental data, manipulation of trees and incorporation  ...  Motivation: Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the  ...  ACKNOWLEDGEMENTS We thank Cathy Lozupone, Jessica Metcalf, Laura Wegener Parfrey, Justin Kuczynski and Jose Clemente for feedback on this manuscript and TopiaryExplorer.  ... 
doi:10.1093/bioinformatics/btr517 pmid:21903626 pmcid:PMC3198578 fatcat:6jzixbcsmzddbeakxxdv2ujxwe

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Kalen Cantrell, Marcus W Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L Beck, Qiyun Zhu (+18 others)
2021 mSystems  
Here we present EMPress, an interactive web tool for visualizing trees in the context of microbiome, metabolome, and other community data scalable to trees with well over 500,000 nodes.  ...  Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees.  ...  We also demonstrate EMPress' ability to annotate large tree visualizations with categorical "feature" (i.e., corresponding to nodes in the tree) metadata: to visualize the relative proportions of taxonomic  ... 
doi:10.1128/msystems.01216-20 pmid:33727399 fatcat:b2zt4xnbnzeajf4hj6hpiker6i

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Kalen Cantrell, Marcus W. Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu (+19 others)
2021 mSystems  
Phylogenetic trees are integral data structures for the analysis of microbial communities.  ...  Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research.  ...  We also demonstrate EMPress' ability to annotate large tree visualizations with categorical "feature" (i.e., corresponding to nodes in the tree) metadata: to visualize the relative proportions of taxonomic  ... 
doi:10.1128/msystems.01216-20 fatcat:jvn4xghvqzbttgskdjodokmt3q

Sequencing our way towards understanding global eukaryotic biodiversity

Holly M. Bik, Dorota L. Porazinska, Simon Creer, J. Gregory Caporaso, Rob Knight, W. Kelley Thomas
2012 Trends in Ecology & Evolution  
Fundamental advances in DNA sequencing and bioinformatics now allow accurate en masse biodiversity assessments of microscopic eukaryotes from environmental samples.  ...  The availability of software such as TopiaryExplorer [67] will greatly aid the visualization and interpretation of OTUs within phylogenetic trees.  ...  High-throughput studies follow a common workflow that begins with raw sequence data and sample metadata (primer barcodes and environmental data).  ... 
doi:10.1016/j.tree.2011.11.010 pmid:22244672 pmcid:PMC3311718 fatcat:qz3sywihsvcdvd4g2utke6kr6m

Evidence for a persistent microbial seed bank throughout the global ocean

S. M. Gibbons, J. G. Caporaso, M. Pirrung, D. Field, R. Knight, J. A. Gilbert
2013 Proceedings of the National Academy of Sciences of the United States of America  
At the L4-DeepSeq site, increasing sequencing depth uncovers greater phylogenetic overlap with the global ICoMM data.  ...  referred to as "phylogenetic gain") for the pooled ICoMM data decreased with respect to the L4-DeepSeq sample (16).  ...  In Fig. 3 , the large phylogenetic tree shows the evolutionary relationships between the abundant (>500 reads) OTUs in the combined ICoMM and L4-DeepSeq dataset, and the smaller trees display the lineages  ... 
doi:10.1073/pnas.1217767110 pmid:23487761 pmcid:PMC3607043 fatcat:4sesdlox3ff57mhkiwi7brolw4

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

Laura Wegener Parfrey, William A. Walters, Christian L. Lauber, Jose C. Clemente, Donna Berg-Lyons, Clotilde Teiling, Chinnappa Kodira, Mohammed Mohiuddin, Julie Brunelle, Mark Driscoll, Noah Fierer, Jack A. Gilbert (+1 others)
2014 Frontiers in Microbiology  
We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment.  ...  We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota  ...  This tree was used for visualization in TopiaryExplorer (Pirrung et al., 2011) , which allows branches to be colored according to sample metadata or taxonomy.  ... 
doi:10.3389/fmicb.2014.00298 pmid:24995004 pmcid:PMC4063188 fatcat:24iz6w7difbgzgwlkcwsci4qla

Effective data visualization for communication and analysis of microbiome data [article]

Megan Pirrung
2021
Both tools provide an intuitive user interface and use informed visual data representations.  ...  Scientists use visualization to both support data analysis and to communicate results to scientific and public audiences.  ...  TopiaryExplorer We have developed the TopiaryExplorer 15 software, a phylogenetic tree viewing tool capable of visualizing large phylogenetic trees and their related metadata.  ... 
doi:10.25677/9mk9-5f96 fatcat:z5o4w3h5gvgavnfenbhjw3zmoa

Advancing Our Understanding of the Human Microbiome Using QIIME [chapter]

José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann (+4 others)
2013 Methods in Enzymology  
High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome.  ...  microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations  ...  The resulting tree file is in Newick format, and can be visualized by programs including TopiaryExplorer (Pirrung, Kennedy, Caporaso, Stombaugh, Wendel, & Knight, 2011) , the R package ape (Paradis,  ... 
doi:10.1016/b978-0-12-407863-5.00019-8 pmid:24060131 pmcid:PMC4517945 fatcat:w6yem3w3szdwteqmqe7t6z7ikq

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

C. Lozupone, K. Faust, J. Raes, J. J. Faith, D. N. Frank, J. Zaneveld, J. I. Gordon, R. Knight
2012 Genome Research  
We aligned sequences with NAST, and built the tree by parsimony insertion into the reference tree from the RDP-II Arb database noted above.  ...  Using phylogenetic relationships to determine genomic characteristics better explained by environmental distribution than phylogeny provides a powerful correction for genomic background .  ...  We aligned representative sequences using NAST (DeSantis et al. 2006) , then added them to a tree containing sequences from the other 464 samples, plus reference tree sequences from the ARB database of  ... 
doi:10.1101/gr.138198.112 pmid:22665442 pmcid:PMC3460192 fatcat:j4vetaghw5c4rcq3pvtsfy2vqi