Weighted normalized UniFrac distances

2018-04-12T19:09:29Z (GMT) by Daniel 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 Abramson
The 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).

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