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Weighted normalized UniFrac distances
dataset
posted on 2018-04-12, 19:09 authored by Daniel McDonaldDaniel McDonald, Daniel McDonald, Adam Robbins-Pianka, Allison E. Mann, Alison Vrbanac, Amnon Amir, Angel Frazier, Antonio Gonzalez, Anupriya Tripathi, Ashkaan K. Fahimipour, Caitriona Brennen, Cameron Martino, Carlito Lebrilla, Catherine Lozupone, Cecil M. Lewis Jr., Charles Raison, Chi Zhang, Christian L. Lauber, Christina Warinner, Christopher A. Lowry, Chris Callewaert, Cinnamon Bloss, Curtis Huttenhower, Dan Knights, Dana Willner, Daniela Domingos Galzerani, David J. Gonzalez, David A. Mills, Deepak Chopra, Dirk Gevers, Donna Berg-Lyons, Dorothy D. Sears, Doug Wendel, Elaine Wolfe, Elijah Lovelace, Embriette R. Hyde, Emily Pierce, Emily TerAvest, Emmanuel Montassier, Evan Bolyen, Frederic D. Bushman, Gail Ackermann, Gary D. Wu, George M. Church, Gholamali Rahnavard, Gordon Saxe, Grant Gogul, Gregory Humphrey, Hannah D. Holscher, Ivo Ugrina, J. Bruce German, J. Gregory Caporaso, Jack Gilbert, Jacob M. Wozniak, Jacqueline Kerr, Jacques Ravel, James Gaffney, James D. Lewis, James T. Morton, Jan S. Suchodolski, Janet K. Jansson, Jarrad T. Hampton-Marcell, Jason Bobe, Jeff Leach, Jeroen Raes, Jessica L. Green, Jessica L. Metcalf, John H. Chase, Jonathan A. Eisen, Jonathan Monk, Jose A. Navas-Molina, Jose C. Clemente, Joseph Petrosino, Joshua Ladau, Joshua Shorenstein, Julia Goodrich, Julia Gauglitz, Julian Jacobs, Justine W. Debelius, Karsten Zengler, Katherine S. Pollard, Kelly S. Swanson, Kim Lewis, Kris Mayer, Kyle Bittinger, Lindsay DeRight Goldasich, Lindsay Dillon, Livia S. Zaramela, Luke R. Thompson, Lynn M. Schriml, Maria G. Dominguez-Bello, Marta M. Jankowska, Martin Blaser, Matthew A. Jackson, Meg Pirrung, Michael Minson, Mike Kurisu, Nadim Ajami, Naseer Sangwan, Neil R. Gottel, Nicholas Chia, Noah Fierer, Owen White, Patrice D. Cani, Paul Wischmeyer, Pawel Gajer, Philip Strandwitz, Phillip Hugenholtz, Pieter C Dorrestein, Purna Kashyap, Rachel Dutton, Rachel S. Park, Ramnik J. Xavier, Rob Knight, Robert R. Dunn, Robert H. Mills, Rosa Krajmalnik-Brown, Ruth Ley, Sarah M. Owens, Scott T. Kelley, Scott Klemmer, Sébastien Matamoros, Shyamal Peddada, Siavash Mirarab, Stefan Janssen, Stephanie Moorman, Susan Holmes, Tara Schwartz, Tifani W. Eshoo-Anton, Tim Vigers, Timothy Spector, Tomasz Kosciolek, Varykina G. Thackray, Vineet Pandey, Will Van Treuren, Xin Fang, Yingfeng Chen, Yoshiki Vázquez-Baeza, Zhenjiang Zech Xu, Alexander A. Aksenov, Alexey V. Melnik, Alan Jarmusch, Justin Geier, Pavel Pevzner, Dmitry Meleshko, Bahar Behsaz, Nicolai Reeve, Ricardo Silva, Qiyun Zhu, Evguenia Kopylova, Clarisse Marotz, Larry Smarr, Tanya Nguyen, Hosein Mohimani, Lingjing Jiang, Austin Swafford, Dominic Nguyen, Se Jin Song, Karenina Sanders, Rodolfo Antonio Salido Benitez, Arthur Cole Heale, Dilip V. Jeste, Tanya T. Nguyen, Brennan, Caitriona, Max AbramsonThe weighted normalized UniFrac distance (Lozupone et al AEM 2007) matrix of the 9511 fecal samples used in the American Gut paper. UniFrac was computed using Striped UniFrac (https://github.com/biocore/unifrac). Prior to execution of UniFrac, Deblur (Amir et al mSystems 2017) was run on the samples, all bloom sOTUs were removed (Amir et al mSystems 2017), and samples were rarefied to a depth of 1250 reads (Weiss et al Microbiome 2017). For the phylogeny, fragments were inserted using SEPP (Mirarab et al Pac Symp Biocomput 2012) into the Greengenes 13_5 99% OTU tree (McDonald et al ISME 2012).
