File:Visualization and diversity metrics from environmental sequencing data.webp

File:Visualization and diversity metrics from environmental sequencing data.webp

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Summary

Description	English: Example of visualization and diversity metrics from environmental sequencing data. a) Alpha diversity displayed as taxonomy bar charts, showing relative abundance of taxa across samples using the Phinch data visualization framework (Bik & Pitch Interactive 2014). b) Beta diversity patterns illustrated via Principal Coordinate Analyses carried out in QIIME (Caporaso et al. 2010), where each dot represents a sample and colors distinguish different classes of sample. The closer two sample points in 3D space, the more similar their community assemblages c) GraPhalAn phylogenetic visualization of environmental data, with circular heatmaps and abundance bars used to convey quantitative taxon traits (figure reproduced from Asnicar et al. 2015) d) Edge PCA, a tree‐based diversity metric that identifies specific lineages (green/orange branches) that contribute most to community changes observed in samples distributed across different PCA axes (Matsen & Evans 2013; figure reproduced from Darling et al. 2014). (2010). "QIIME allows analysis of high-throughput community sequencing data". Nature Methods 7 (5): 335–336. DOI:10.1038/nmeth.f.303. PMID 20383131. PMC: 3156573. (2015). "Compact graphical representation of phylogenetic data and metadata with GraPhl An". PeerJ 3: e1029. DOI:10.7717/peerj.1029. PMID 26157614. PMC: 4476132. (2013). "Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison". PLOS ONE 8 (3): e56859. DOI:10.1371/journal.pone.0056859. PMID 23505415. PMC: 3594297. (2014). "Phylo Sift: Phylogenetic analysis of genomes and metagenomes". PeerJ 2: e243. DOI:10.7717/peerj.243. PMID 24482762. PMC: 3897386.
Date	5 April 2016
Source	[1] doi:10.1111/2041-210X.12574
Author	Simon Creer, Kristy Deiner, Serita Frey, Dorota Porazinska, Pierre Taberlet, W. Kelley Thomas, Caitlin Potter and Holly M. Bik

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