%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


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@article{fukuyama2012com,
	Abstract = {This article compares different methods for combining abundance data, phylogenetic trees and clinical covariates in a nonparametric setting. In particular we study the output from the principal coordinates analysis on UNIFRAC and WEIGHTED UNIFRAC distances and the output from a double principal coordinate analyses DPCOA using distances computed on the phylogenetic tree. We also present power comparisons for some of the standard tests of phylogenetic signal between different types of samples. These methods are compared both on simulated and real data sets. Our study shows that DPCoA is less robust to outliers, and more robust to small noisy fluctuations around zero. },
	Author = {Fukuyama, J. and McMurdie, P.J. and Dethlefsen, L. and Relman, D.A. and Holmes, S.},
	Date-Added = {2012-03-16 11:52:11 -0700},
	Date-Modified = {2012-03-16 11:52:11 -0700},
	Journal = {Pac Symp Biocomput},
	Title = {Comparisons of distance methods for combining covariates and abundances in microbiome studies.},
	Year = {2012}}

@article{mcmurdie2012phy,
	Abstract = {We present a detailed description of a new Bioconductor package, phyloseq, for integrated data and analysis of taxonomically-clustered phylogenetic sequencing data in conjunction with related data types. The phyloseq package integrates abundance data, phylogenetic information and covariates so that exploratory transformations, plots, and confirmatory testing and diagnostic plots can be carried out seamlessly. The package is built following the S4 object-oriented framework of the R language so that once the data have been input the user can easily transform, plot and analyze the data. We present some examples that highlight the methods and the ease with which we can leverage existing packages. },
	Author = {McMurdie, P.J. and Holmes, S.},
	Date-Added = {2012-03-16 11:52:00 -0700},
	Date-Modified = {2012-03-16 11:52:00 -0700},
	Journal = {Pac Symp Biocomput},
	Title = {Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data.},
	Year = {2012}}

@article{Pavoine2004523,
	Author = {Sandrine Pavoine and Anne-B{\'e}atrice Dufour and Daniel Chessel},
	Date-Added = {2012-03-15 18:21:11 +0000},
	Date-Modified = {2012-03-15 18:21:11 +0000},
	Doi = {10.1016/j.jtbi.2004.02.014},
	Issn = {0022-5193},
	Journal = {Journal of Theoretical Biology},
	Keywords = {PCoA},
	Number = {4},
	Pages = {523 - 537},
	Title = {From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis},
	Url = {http://www.sciencedirect.com/science/article/pii/S0022519304000736},
	Volume = {228},
	Year = {2004},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0022519304000736},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jtbi.2004.02.014}}

@article{Arumugam:2011fk,
	Annote = {10.1038/nature09944},
	Author = {Arumugam, Manimozhiyan and Raes, Jeroen and Pelletier, Eric and Le Paslier, Denis and Yamada, Takuji and Mende, Daniel R. and Fernandes, Gabriel R. and Tap, Julien and Bruls, Thomas and Batto, Jean-Michel and Bertalan, Marcelo and Borruel, Natalia and Casellas, Francesc and Fernandez, Leyden and Gautier, Laurent and Hansen, Torben and Hattori, Masahira and Hayashi, Tetsuya and Kleerebezem, Michiel and Kurokawa, Ken and Leclerc, Marion and Levenez, Florence and Manichanh, Chaysavanh and Nielsen, H. Bjorn and Nielsen, Trine and Pons, Nicolas and Poulain, Julie and Qin, Junjie and Sicheritz-Ponten, Thomas and Tims, Sebastian and Torrents, David and Ugarte, Edgardo and Zoetendal, Erwin G. and Wang, Jun and Guarner, Francisco and Pedersen, Oluf and de Vos, Willem M. and Brunak, Soren and Dore, Joel and Weissenbach, Jean and Ehrlich, S. Dusko and Bork, Peer},
	Date = {2011/05/12/print},
	Date-Added = {2012-02-22 16:04:26 -0800},
	Date-Modified = {2012-02-22 16:04:26 -0800},
	Day = {12},
	Isbn = {0028-0836},
	Journal = {Nature},
	L3 = {http://www.nature.com/nature/journal/v473/n7346/abs/10.1038-nature09944-unlocked.html#supplementary-information},
	M3 = {10.1038/nature09944},
	Month = {05},
	Number = {7346},
	Pages = {174--180},
	Publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	Title = {Enterotypes of the human gut microbiome},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1038/nature09944},
	Volume = {473},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/nature09944}}

@article{Koleff2003JAE,
	Abstract = {
* 1Little consensus has been reached as to general features of spatial variation in beta diversity, a fundamental component of species diversity. This could reflect a genuine lack of simple gradients in beta diversity, or a lack of agreement as to just what constitutes beta diversity. Unfortunately, a large number of approaches have been applied to the investigation of variation in beta diversity, which potentially makes comparisons of the findings difficult.
* 2We review 24 measures of beta diversity for presence/absence data (the most frequent form of data to which such measures are applied) that have been employed in the literature, express many of them for the first time in common terms, and compare some of their basic properties.
* 3Four groups of measures are distinguished, with a fundamental distinction arising between `broad sense' measures incorporating differences in composition attributable to species richness gradients, and `narrow sense' measures that focus on compositional differences independent of such gradients. On a number of occasions on which the former have been employed in the literature the latter may have been more appropriate, and there are many situations in which consideration of both kinds of measures would be valuable.
* 4We particularly recommend (i) considering beta diversity measures in terms of matching/mismatching components (usually denoted a, b and c) and thereby identifying the contribution of different sources of variation in species composition, and (ii) the use of ternary plots to express the relationship between the values of these measures and of the components, and as a way of understanding patterns in beta diversity.},
	Author = {Koleff, Patricia and Gaston, Kevin J. and Lennon, Jack J.},
	Date-Added = {2012-02-17 16:49:06 -0800},
	Date-Modified = {2012-02-17 16:49:43 -0800},
	Doi = {10.1046/j.1365-2656.2003.00710.x},
	Issn = {1365-2656},
	Journal = {Journal of Animal Ecology},
	Keywords = {beta diversity, biodiversity, presence--absence, similarity indices, spatial turnover},
	Number = {3},
	Pages = {367--382},
	Publisher = {Blackwell Science Ltd},
	Title = {Measuring beta diversity for presence--absence data},
	Url = {http://dx.doi.org/10.1046/j.1365-2656.2003.00710.x},
	Volume = {72},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1046/j.1365-2656.2003.00710.x}}

@article{Caporaso15032011,
	Abstract = {The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known ``mock communities'' at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.},
	Author = {Caporaso, J. Gregory and Lauber, Christian L. and Walters, William A. and Berg-Lyons, Donna and Lozupone, Catherine A. and Turnbaugh, Peter J. and Fierer, Noah and Knight, Rob},
	Date-Added = {2012-02-17 12:19:05 -0800},
	Date-Modified = {2012-02-17 12:19:05 -0800},
	Doi = {10.1073/pnas.1000080107},
	Eprint = {http://www.pnas.org/content/108/suppl.1/4516.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {Supplement 1},
	Pages = {4516-4522},
	Title = {Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample},
	Url = {http://www.pnas.org/content/108/suppl.1/4516.abstract},
	Volume = {108},
	Year = {2011},
	Bdsk-Url-1 = {http://www.pnas.org/content/108/suppl.1/4516.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.1000080107}}

@manual{multtest,
	Author = {Katherine S. Pollard and Houston N. Gilbert and Yongchao Ge and Sandra Taylor and Sandrine Dudoit},
	Date-Added = {2012-02-16 17:18:18 -0800},
	Date-Modified = {2012-02-16 17:18:18 -0800},
	Note = {R package version 2.10.0},
	Title = {multtest: Resampling-based multiple hypothesis testing}}

@article{Hamady:2009fk,
	Author = {Hamady, Micah and Lozupone, Catherine and Knight, Rob},
	Date = {2009/08/27/online},
	Date-Added = {2012-02-16 16:20:22 -0800},
	Date-Modified = {2012-02-16 16:20:22 -0800},
	Day = {27},
	Isbn = {1751-7362},
	Journal = {ISME J},
	L3 = {http://www.nature.com/ismej/journal/v4/n1/suppinfo/ismej200997s1.html},
	Month = {08},
	Number = {1},
	Pages = {17--27},
	Publisher = {International Society for Microbial Ecology},
	Title = {Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1038/ismej.2009.97},
	Volume = {4},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1038/ismej.2009.97}}

@book{ggplot2,
	Author = {Hadley Wickham},
	Date-Added = {2011-07-13 18:02:05 -0700},
	Date-Modified = {2011-07-13 18:02:05 -0700},
	Isbn = {978-0-387-98140-6},
	Publisher = {Springer New York},
	Title = {ggplot2: elegant graphics for data analysis},
	Url = {http://had.co.nz/ggplot2/book},
	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},
	Month = jul,
	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 (Oxford, England)},
	Month = feb,
	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 (Oxford, England)},
	Month = jul,
	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},
	Month = jul,
	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 = {2011-07-11 10:00:45 -0700},
	Journal = {Applied and environmental microbiology},
	Month = jul,
	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 = {2011-07-11 09:46:43 -0700},
	Journal = {Nature reviews Genetics},
	Month = jan,
	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 = {2011-07-11 09:46:43 -0700},
	Journal = {Nature methods},
	Month = mar,
	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 = {2011-07-11 09:46:43 -0700},
	Journal = {Science (New York, NY)},
	Month = may,
	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},
	Month = jan,
	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 = {2011-07-08 10:40:20 -0700},
	Publisher = {Springer Verlag},
	Series = {programming with R},
	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},
	Month = mar,
	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 (Oxford, England)},
	Month = feb,
	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 (Oxford, England)},
	Month = jul,
	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},
	Month = jun,
	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 (Oxford, England)},
	Month = apr,
	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},
	Month = feb,
	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},
	Journal = {Pacific Symposium on Biocomputing. 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},
	Month = sep,
	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},
	Month = jul,
	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 (Oxford, England)},
	Month = may,
	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},
	Month = may,
	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},
	Month = feb,
	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},
	Month = nov,
	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},
	Month = jan,
	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},
	Month = oct,
	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},
	Journal = {BMC Bioinformatics},
	Pages = {371},
	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},
	Month = dec,
	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 (Oxford, England)},
	Month = jan,
	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},
	Note = {R package version 1.17-10},
	Title = {vegan: Community Ecology Package},
	Url = {http://CRAN.R-project.org/package=vegan},
	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)},
	Note = {R package version 0.6.3},
	Title = {phylobase: Base package for phylogenetic structures and comparative data},
	Url = {http://CRAN.R-project.org/package=phylobase},
	Year = {2011},
	Bdsk-Url-1 = {http://CRAN.R-project.org/package=phylobase}}

@manual{Rlanguage,
	Address = {Vienna, Austria},
	Author = {{R Development Core Team}},
	Note = {{ISBN} 3-900051-07-0},
	Organization = {R Foundation for Statistical Computing},
	Title = {R: A Language and Environment for Statistical Computing},
	Url = {http://www.R-project.org/},
	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}},
	Journal = {Genome Biology},
	Pages = {R80},
	Title = {Bioconductor: Open software development for computational biology and bioinformatics},
	Url = {http://genomebiology.com/2004/5/10/R80},
	Volume = {5},
	Year = {2004},
	Bdsk-Url-1 = {http://genomebiology.com/2004/5/10/R80}}

@manual{Rmpipkg,
	Author = {Hao Yu},
	Note = {R package version 0.5-9},
	Title = {Rmpi: Interface (Wrapper) to MPI (Message-Passing Interface)},
	Url = {http://CRAN.R-project.org/package=Rmpi},
	Year = {2010},
	Bdsk-Url-1 = {http://CRAN.R-project.org/package=Rmpi}}

@article{CCA,
	Abstract = {{Canonical correspondence analysis (CCA) is introduced
as a multivariate extension of weighted averaging ordination, which is
a simple method for arranging species along environmental variables.
CCA constructs those linear combinations of environmental variables,
along which the distributions of the species are maximally separated.
The eigenvalues produced by CCA measure this separation.}},
	Author = {Ter Braak, Cajo J. F.},
	Doi = {10.1007/BF00038688},
	Issn = {0042-3106},
	Journal = {Plant Ecology},
	Keywords = {dca},
	Month = apr,
	Number = {1},
	Pages = {69--77},
	Posted-At = {2011-05-27 07:06:54},
	Priority = {2},
	Publisher = {Springer Netherlands},
	Title = {{The analysis of vegetation-environment relationships by canonical correspondence analysis}},
	Url = {http://dx.doi.org/10.1007/BF00038688},
	Volume = {69},
	Year = {1987},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00038688}}
