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@proceedings{phyloseqPSB,
	Author = {{Paul J. McMurdie} and {Susan Holmes}},
	Date-Added = {2011-10-28 17:26:24 +0000},
	Date-Modified = {2011-10-28 17:31:24 +0000},
	Organization = {Pacific Symposium on Biocomputing},
	Pages = {235-246},
	Title = {{phyloseq: A Bioconductor Package for Handling and Analysis of High-Throughput Phylogenetic Sequence Data}},
	Url = {{http://psb.stanford.edu/psb-online/proceedings/psb12/mcmurdie.pdf}},
	Volume = {17},
	Year = {2012}}

@manual{foreach,
	Author = {{Revolution Analytics}},
	Date-Added = {2011-10-28 16:54:08 +0000},
	Date-Modified = {2011-10-28 17:00:48 +0000},
	Note = {{R package version 1.3.2}},
	Title = {{foreach: Foreach looping construct for R}},
	Url = {{http://CRAN.R-project.org/package=foreach}},
	Year = {2011}}

@book{ggplot2,
	Author = {Hadley Wickham},
	Date-Added = {2011-07-13 18:02:05 -0700},
	Date-Modified = {2011-09-28 17:12:19 +0000},
	Isbn = {978-0-387-98140-6},
	Publisher = {Springer New York},
	Title = {ggplot2: elegant graphics for data analysis},
	Year = {2009},
	Bdsk-Url-1 = {http://had.co.nz/ggplot2/book}}

@article{Hamady:2009fl,
	Author = {Hamady, Micah and Knight, Rob},
	Date-Added = {2011-07-11 10:39:58 -0700},
	Date-Modified = {2011-07-11 10:39:58 -0700},
	Journal = {Genome Research},
	Number = {7},
	Pages = {1141--1152},
	Title = {{Microbial community profiling for human microbiome projects: Tools, techniques, and challenges.}},
	Volume = {19},
	Year = {2009}}

@article{Huang:2010jb,
	Author = {Huang, Y and Niu, B and Gao, Y and Fu, L and Li, W},
	Date-Added = {2011-07-11 10:39:58 -0700},
	Date-Modified = {2011-07-11 10:39:58 -0700},
	Journal = {Bioinformatics},
	Number = {5},
	Pages = {680--682},
	Title = {{CD-HIT Suite: a web server for clustering and comparing biological sequences}},
	Volume = {26},
	Year = {2010}}

@article{Li:2006hr,
	Author = {Li, Weizhong and Godzik, Adam},
	Date-Added = {2011-07-11 10:39:58 -0700},
	Date-Modified = {2011-07-11 10:39:58 -0700},
	Journal = {Bioinformatics},
	Number = {13},
	Pages = {1658--1659},
	Title = {{Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.}},
	Volume = {22},
	Year = {2006}}

@article{Pruesse:2007jc,
	Author = {Pruesse, Elmar and Quast, Christian and Knittel, Katrin and Fuchs, Bernhard M and Ludwig, Wolfgang and Peplies, J{\"o}rg and Gl{\"o}ckner, Frank Oliver},
	Date-Added = {2011-07-11 10:00:45 -0700},
	Date-Modified = {2011-07-11 10:00:45 -0700},
	Journal = {Nucleic Acids Research},
	Number = {21},
	Pages = {7188--7196},
	Title = {{SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB.}},
	Volume = {35},
	Year = {2007}}

@article{DeSantis:2006kj,
	Author = {DeSantis, T Z and Hugenholtz, P and Keller, K and Brodie, E L and Larsen, N and Piceno, Y M and Phan, R and Andersen, G L},
	Date-Added = {2011-07-11 10:00:45 -0700},
	Date-Modified = {2011-07-11 10:00:45 -0700},
	Journal = {Nucleic Acids Research},
	Number = {Web Server issue},
	Pages = {W394--9},
	Title = {{NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes.}},
	Volume = {34},
	Year = {2006}}

@article{DeSantis:2006ii,
	Author = {DeSantis, T Z and Hugenholtz, P and Larsen, N and Rojas, M and Brodie, E L and Keller, K and Huber, T and Dalevi, D and Hu, P and Andersen, G L},
	Date-Added = {2011-07-11 10:00:45 -0700},
	Date-Modified = {2011-09-28 17:27:47 +0000},
	Journal = {Applied and Environmental Microbiology},
	Number = {7},
	Pages = {5069--5072},
	Title = {{Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.}},
	Volume = {72},
	Year = {2006}}

@article{Metzker:2010ew,
	Author = {Metzker, Michael L},
	Date-Added = {2011-07-11 09:46:43 -0700},
	Date-Modified = {2011-09-28 17:23:21 +0000},
	Journal = {Nature Reviews Genetics},
	Number = {1},
	Pages = {31--46},
	Title = {{Sequencing technologies - the next generation.}},
	Volume = {11},
	Year = {2010}}

@article{Hamady:2008iu,
	Author = {Hamady, Micah and Walker, Jeffrey J and Harris, J Kirk and Gold, Nicholas J and Knight, Rob},
	Date-Added = {2011-07-11 09:46:43 -0700},
	Date-Modified = {2011-09-28 17:23:48 +0000},
	Journal = {Nature Methods},
	Number = {3},
	Pages = {235--237},
	Title = {{Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.}},
	Volume = {5},
	Year = {2008}}

@article{Pace:1997tl,
	Author = {Pace, N R},
	Date-Added = {2011-07-11 09:46:43 -0700},
	Date-Modified = {2011-09-28 17:25:18 +0000},
	Journal = {Science},
	Number = {5313},
	Pages = {734--740},
	Title = {{A molecular view of microbial diversity and the biosphere.}},
	Volume = {276},
	Year = {1997}}

@book{Holmes:2008ck,
	Address = {Beachwood, Ohio, USA},
	Author = {Holmes, Susan},
	Date-Added = {2011-07-08 16:49:11 -0700},
	Date-Modified = {2011-07-08 16:49:11 -0700},
	Editor = {Nolan, Deborah and Speed, Terry},
	Publisher = {Institute of Mathematical Statistics},
	Title = {{Multivariate Analysis: The French Way}},
	Volume = {2},
	Year = {2008}}

@article{Dray:2007vs,
	Author = {Dray, S},
	Date-Added = {2011-07-08 10:58:38 -0700},
	Date-Modified = {2011-07-08 10:58:38 -0700},
	Journal = {Journal of Statistical Software},
	Title = {{The ade4 package: implementing the duality diagram for ecologists}},
	Year = {2007}}

@book{Chambers:2008wi,
	Author = {Chambers, John M},
	Date-Added = {2011-07-08 10:40:20 -0700},
	Date-Modified = {2011-09-28 17:17:59 +0000},
	Publisher = {Springer Verlag},
	Title = {{Software for data analysis}},
	Year = {2008}}

@article{Lozupone:2007kg,
	Author = {Lozupone, Catherine A and Hamady, Micah and Kelley, Scott T and Knight, Rob},
	Date-Added = {2011-07-07 11:42:04 -0700},
	Date-Modified = {2011-07-07 11:42:04 -0700},
	Journal = {Applied and Environmental Microbiology},
	Number = {5},
	Pages = {1576--1585},
	Title = {{Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.}},
	Volume = {73},
	Year = {2007}}

@article{Schliep:2011hh,
	Author = {Schliep, Klaus Peter},
	Date-Added = {2011-07-07 11:32:43 -0700},
	Date-Modified = {2011-07-07 11:32:43 -0700},
	Journal = {Bioinformatics},
	Number = {4},
	Pages = {592--593},
	Title = {{phangorn: phylogenetic analysis in R.}},
	Volume = {27},
	Year = {2011}}

@article{Jombart:2010fe,
	Author = {Jombart, T and Balloux, F and Dray, S},
	Date-Added = {2011-07-07 11:19:54 -0700},
	Date-Modified = {2011-07-07 11:19:54 -0700},
	Journal = {Bioinformatics},
	Number = {15},
	Pages = {1907--1909},
	Title = {{adephylo: new tools for investigating the phylogenetic signal in biological traits}},
	Volume = {26},
	Year = {2010}}

@article{Werner:2011jm,
	Author = {Werner, Jeffrey J and Koren, Omry and Hugenholtz, Philip and DeSantis, Todd Z and Walters, William A and Caporaso, J Gregory and Angenent, Largus T and Knight, Rob and Ley, Ruth E},
	Journal = {The ISME Journal},
	Title = {{Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.}},
	Year = {2011}}

@article{Beck:2011dc,
	Author = {Beck, D and Settles, M and Foster, J A},
	Journal = {Bioinformatics},
	Title = {{OTUbase: an R infrastructure package for operational taxonomic unit data}},
	Year = {2011}}

@article{Zhou:2011gb,
	Author = {Zhou, Jizhong and Wu, Liyou and Deng, Ye and Zhi, Xiaoyang and Jiang, Yi-Huei and Tu, Qichao and Xie, Jianping and van Nostrand, Joy D and He, Zhili and Yang, Yunfeng},
	Journal = {The ISME Journal},
	Title = {{Reproducibility and quantitation of amplicon sequencing-based detection}},
	Year = {2011}}

@article{Holmes:2011vb,
	Author = {Holmes, Susan and Alekseyenko, Alexander and Timme, Alden and Nelson, Tyrrell and Pasricha, Pankaj Jay and Spormann, Alfred},
	Date-Modified = {2011-09-28 19:12:42 +0000},
	Journal = {Pacific Symposium on Biocomputing},
	Pages = {142--153},
	Title = {{Visualization and statistical comparisons of microbial communities using R packages on phylochip data.}},
	Year = {2011}}

@article{Lozupone:2010dh,
	Author = {Lozupone, Catherine and Lladser, Manuel E and Knights, Dan and Stombaugh, Jesse and Knight, Rob},
	Journal = {The ISME Journal},
	Title = {{UniFrac: an effective distance metric for microbial community comparison}},
	Year = {2010}}

@article{Giongo:2010bv,
	Author = {Giongo, Adriana and Crabb, David B and Davis-Richardson, Austin G and Chauliac, Diane and Mobberley, Jennifer M and Gano, Kelsey A and Mukherjee, Nabanita and Casella, George and Roesch, Luiz F W and Walts, Brandon and Riva, Alberto and King, Gary and Triplett, Eric W},
	Journal = {The ISME Journal},
	Number = {7},
	Pages = {852--861},
	Title = {{PANGEA: pipeline for analysis of next generation amplicons.}},
	Volume = {4},
	Year = {2010}}

@article{Kembel:2010ft,
	Author = {Kembel, S W and Cowan, P D and Helmus, M R and Cornwell, W K and Morlon, H and Ackerly, D D and Blomberg, S P and Webb, C O},
	Journal = {Bioinformatics},
	Number = {11},
	Pages = {1463--1464},
	Title = {{Picante: R tools for integrating phylogenies and ecology}},
	Volume = {26},
	Year = {2010}}

@article{Caporaso:2010jf,
	Author = {Caporaso, J Gregory and Kuczynski, Justin and Stombaugh, Jesse and Bittinger, Kyle and Bushman, Frederic D and Costello, Elizabeth K and Fierer, Noah and Pe{\~n}a, Antonio Gonzalez and Goodrich, Julia K and Gordon, Jeffrey I and Huttley, Gavin A and Kelley, Scott T and Knights, Dan and Koenig, Jeremy E and Ley, Ruth E and Lozupone, Catherine A and McDonald, Daniel and Muegge, Brian D and Pirrung, Meg and Reeder, Jens and Sevinsky, Joel R and Turnbaugh, Peter J and Walters, William A and Widmann, Jeremy and Yatsunenko, Tanya and Zaneveld, Jesse and Knight, Rob},
	Journal = {Nature Methods},
	Number = {5},
	Pages = {335--336},
	Title = {{QIIME allows analysis of high-throughput community sequencing data}},
	Volume = {7},
	Year = {2010}}

@article{Wooley:2010uv,
	Author = {Wooley, John C and Godzik, Adam and Friedberg, Iddo},
	Journal = {PLoS Computational Biology},
	Number = {2},
	Pages = {e1000667},
	Title = {{A Primer on Metagenomics}},
	Volume = {6},
	Year = {2010}}

@article{Thioulouse:2010vl,
	Author = {Thioulouse, J},
	Journal = {Annals of Applied Statistics},
	Title = {{Simultaneous analysis of a sequence of paired ecological tables: A comparison of several methods}},
	Year = {2010}}

@article{Schloss:2009do,
	Author = {Schloss, P D and Westcott, S L and Ryabin, T and Hall, J R and Hartmann, M and Hollister, E B and Lesniewski, R A and Oakley, B B and Parks, D H and Robinson, C J and Sahl, J W and Stres, B and Thallinger, G G and Van Horn, D J and Weber, C F},
	Journal = {Applied and Environmental Microbiology},
	Number = {23},
	Pages = {7537--7541},
	Title = {{Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities}},
	Volume = {75},
	Year = {2009}}

@article{Cole:2009dm,
	Author = {Cole, J R and Wang, Q and Cardenas, E and Fish, J and Chai, B and Farris, R J and Kulam-Syed-Mohideen, A S and McGarrell, D M and Marsh, T and Garrity, G M and Tiedje, J M},
	Journal = {Nucleic Acids Research},
	Number = {Database issue},
	Pages = {D141--5},
	Title = {{The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.}},
	Volume = {37},
	Year = {2009}}

@article{Liu:2008bi,
	Author = {Liu, Zongzhi and DeSantis, Todd Z and Andersen, Gary L and Knight, Rob},
	Journal = {Nucleic Acids Research},
	Number = {18},
	Pages = {e120},
	Title = {{Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers.}},
	Volume = {36},
	Year = {2008}}

@article{Lozupone:2006is,
	Author = {Lozupone, Catherine and Hamady, Micah and Knight, Rob},
	Date-Modified = {2011-09-28 17:20:15 +0000},
	Journal = {BMC Bioinformatics},
	Title = {{UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context}},
	Volume = {7},
	Year = {2006}}

@article{Lozupone:2005gn,
	Author = {Lozupone, Catherine and Knight, Rob},
	Journal = {Applied and Environmental Microbiology},
	Number = {12},
	Pages = {8228--8235},
	Title = {{UniFrac: a new phylogenetic method for comparing microbial communities.}},
	Volume = {71},
	Year = {2005}}

@article{Paradis:2004ws,
	Author = {Paradis, Emmanuel and Claude, Julien and Strimmer, Korbinian},
	Journal = {Bioinformatics},
	Number = {2},
	Pages = {289--290},
	Title = {{APE: Analyses of Phylogenetics and Evolution in R language.}},
	Volume = {20},
	Year = {2004}}

@manual{veganpkg,
	Author = {Jari Oksanen and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Helene Wagner},
	Date-Modified = {2011-09-28 17:12:20 +0000},
	Note = {R package version 1.17-10},
	Title = {vegan: Community Ecology Package},
	Year = {2011},
	Bdsk-Url-1 = {http://CRAN.R-project.org/package=vegan}}

@manual{phylobasepkg,
	Author = {R Hackathon et al. (alphabetically: Ben Bolker and Marguerite Butler and Peter Cowan and Damien de Vienne and Dirk Eddelbuettel and Mark Holder and Thibaut Jombart and Steve Kembel and Francois Michonneau and David Orme and Brian O'Meara and Emmanuel Paradis and Jim Regetz and Derrick Zwickl)},
	Date-Modified = {2011-09-28 17:12:20 +0000},
	Note = {R package version 0.6.3},
	Title = {phylobase: Base package for phylogenetic structures and comparative data},
	Year = {2011},
	Bdsk-Url-1 = {http://CRAN.R-project.org/package=phylobase}}

@manual{Rlanguage,
	Address = {Vienna, Austria},
	Author = {{R Development Core Team}},
	Date-Modified = {2011-09-28 17:12:20 +0000},
	Note = {{ISBN} 3-900051-07-0},
	Organization = {R Foundation for Statistical Computing},
	Title = {R: A Language and Environment for Statistical Computing},
	Year = {2011},
	Bdsk-Url-1 = {http://www.R-project.org/}}

@article{Bioconductor,
	Author = {Robert C Gentleman and Vincent J. Carey and Douglas M. Bates and {others}},
	Date-Modified = {2011-09-28 17:12:20 +0000},
	Journal = {Genome Biology},
	Pages = {R80},
	Title = {Bioconductor: Open software development for computational biology and bioinformatics},
	Volume = {5},
	Year = {2004},
	Bdsk-Url-1 = {http://genomebiology.com/2004/5/10/R80}}

@manual{Rmpipkg,
	Author = {Hao Yu},
	Date-Modified = {2011-09-28 17:12:20 +0000},
	Note = {R package version 0.5-9},
	Title = {Rmpi: Interface (Wrapper) to MPI (Message-Passing Interface)},
	Year = {2010},
	Bdsk-Url-1 = {http://CRAN.R-project.org/package=Rmpi}}

@article{CCA,
	Author = {Ter Braak, Cajo J. F.},
	Date-Modified = {2011-09-28 17:12:20 +0000},
	Journal = {Plant Ecology},
	Number = {1},
	Pages = {69--77},
	Title = {{The analysis of vegetation-environment relationships by canonical correspondence analysis}},
	Volume = {69},
	Year = {1987},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00038688}}
