bibtexlib_old1.bib

@article{danecek2011variant,
  title={The variant call format and {VCF}tools},
  author={Danecek, Petr and Auton, Adam and Abecasis, Goncalo and Albers, Cornelis A and Banks, Eric and DePristo, Mark A and Handsaker, Robert E and Lunter, Gerton and Marth, Gabor T and Sherry, Stephen T and others},
  journal={Bioinformatics},
  volume={27},
  number={15},
  pages={2156--2158},
  year={2011},
  publisher={Oxford Univ Press}
}

@article{hedrick2005standardized,
  title={A standardized genetic differentiation measure},
  author={Hedrick, Philip W},
  journal={Evolution},
  volume={59},
  number={8},
  pages={1633--1638},
  year={2005},
  url = {http://dx.doi.org/10.1111/j.0014-3820.2005.tb01814.x},
  publisher={BioOne}
}

@article{jost2008gst,
  title={$G_{ST}$ and its relatives do not measure differentiation},
  author={Jost, Lou},
  journal={Molecular Ecology},
  volume={17},
  number={18},
  pages={4015--4026},
  year={2008},
  url = {http://dx.doi.org/10.1111/j.1365-294X.2008.03887.x},
  publisher={Wiley Online Library}
}

@article{nei1973analysis,
  title={Analysis of gene diversity in subdivided populations},
  author={Nei, Masatoshi},
  journal={Proceedings of the National Academy of Sciences},
  volume={70},
  number={12},
  pages={3321--3323},
  year={1973},
  URL = {http://www.pnas.org/content/70/12/3321.abstract},
  publisher={National Acad Sciences}
}

@article{luikart2003power,
  title={The power and promise of population genomics: from genotyping to genome typing},
  author={Luikart, Gordon and England, Phillip R and Tallmon, David and Jordan, Steve and Taberlet, Pierre},
  journal={Nature reviews genetics},
  volume={4},
  number={12},
  pages={981--994},
  year={2003},
  DOI={10.1038/nrg1226},
  URL={http://www.nature.com/nrg/journal/v4/n12/full/nrg1226.html},
  publisher={Nature Publishing Group}
}

@article{nei1973analysis,
  title={Analysis of gene diversity in subdivided populations},
  author={Nei, Masatoshi},
  journal={Proceedings of the National Academy of Sciences},
  volume={70},
  number={12},
  pages={3321--3323},
  year={1973},
  publisher={National Acad Sciences}
}

@article{paradis2004ape,
  title={APE: analyses of phylogenetics and evolution in R language},
  author={Paradis, Emmanuel and Claude, Julien and Strimmer, Korbinian},
  journal={Bioinformatics},
  volume={20},
  number={2},
  pages={289--290},
  DOI={10.1093/bioinformatics/btg412},
  URL={https://doi.org/10.1093/bioinformatics/btg412},
  year={2004},
  publisher={Oxford Univ Press}
}

@article{simpson1949measurement,
  title={Measurement of diversity.},
  author={Simpson, Edward H},
  journal={Nature},
  year={1949},
  volume=163,
  pages={688},
  url = {http://dx.doi.org/10.1038/163688a0},
}


@article{wright1949genetical,
  title={The genetical structure of populations},
  author={Wright, Sewall},
  journal={Annals of Eugenics},
  volume={15},
  number={1},
  pages={323--354},
  year={1949},
  publisher = {Blackwell Publishing Ltd},
  issn = {2050-1439},
  url = {http://dx.doi.org/10.1111/j.1469-1809.1949.tb02451.x},
  doi = {10.1111/j.1469-1809.1949.tb02451.x},
}


@article{jombart2008adegenet,
  title={adegenet: a R package for the multivariate analysis of genetic markers},
  author={Jombart, Thibaut},
  journal={Bioinformatics},
  volume={24},
  number={11},
  pages={1403--1405},
  year={2008},
  URL={https://doi.org/10.1093/bioinformatics/btn129},
  DOI={10.1093/bioinformatics/btn129},
  publisher={Oxford Univ Press}
}

@article{paradis2017towards,
  title={Towards an integrated ecosystem of R packages for the analysis of population genetic data},
  author={Paradis, Emmanuel and Gosselin, Thierry and Gr{\"u}nwald, Niklaus J and Jombart, Thibaut and Manel, St{\'e}phanie and Lapp, Hilmar},
  journal={Molecular Ecology Resources},
  volume={17},
  number={1},
  pages={1--4},
  year={2017},
  URL={http://dx.doi.org/10.1111/1755-0998.12636},
  DOI={10.1111/1755-0998.12636},
  publisher={Wiley Online Library}
}

@article{grunwald2016population,
  title={Population genomics of fungal and oomycete pathogens},
  author={Gr{\"u}nwald, Niklaus J and McDonald, Bruce A and Milgroom, Michael G},
  journal={Annual review of phytopathology},
  volume={54},
  pages={323--346},
  year={2016},
  URL={http://arjournals.annualreviews.org/doi/full/10.1146/annurev-phyto-080614-115913},
  DOI={0.1146/annurev-phyto-080614-115913},
  publisher={Annual Reviews}
}

@article{kamvar2015novel,
  title={Novel {R} tools for analysis of genome-wide population genetic data with emphasis on clonality},
  author={Kamvar, Zhian N and Brooks, Jonah C and Gr{\"u}nwald, Niklaus J},
  journal={Frontiers in Genetics},
  volume={6},
  pages={208},
  year={2015},
  DOI={10.3389/fgene.2015.00208},
  URL={https://doi.org/10.3389/fgene.2015.00208},
  publisher={Frontiers Media SA}
}

@article{knaus2017vcfr,
  title={vcfr: a package to manipulate and visualize variant call format data in R},
  author={Knaus, Brian J and Gr{\"u}nwald, Niklaus J},
  journal={Molecular Ecology Resources},
  volume={17},
  number={1},
  pages={44--53},
  year={2017},
  URL={http://dx.doi.org/10.1111/1755-0998.12549},
  publisher={Wiley Online Library}
}

@article{simpson1949measurement,
  author = {Simpson, E.H.},
  journal = {Nature},
  number = 4148,
  pages = 688,
  publisher = {Nature Publishing Group},
  title = {Measurement of diversity},
  volume = 163,
  year = 1949
}

@article{goss2009population,
  title={Population genetic analysis infers migration pathways of Phytophthora ramorum in US nurseries},
  author={Goss, Erica M and Larsen, Meg and Chastagner, Gary A and Givens, Donald R and Gr{\"u}nwald, Niklaus J},
  journal={PLoS Pathog},
  volume={5},
  number={9},
  pages={e1000583},
  year={2009},
  url={http://dx.doi.org/10.1371/journal.ppat.1000583},
  doi={10.1371/journal.ppat.1000583}
}

@article{kamvar2015spatial,
  title={Spatial and temporal analysis of populations of the sudden oak death pathogen in Oregon forests},
  author={Kamvar, ZN and Larsen, MM and Kanaskie, AM and Hansen, EM and Gr{\"u}nwald, NJ},
  journal={Phytopathology},
  pages={PHYTO--12},
  year={2015},
  publisher={Am Phytopath Society},
  url={http://dx.doi.org/10.1094/PHYTO-12-14-0350-FI},
  doi={10.1094/PHYTO-12-14-0350-FI}
}

@article{kamvar2015novel,
  title={{Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality}},
  author={Kamvar, Zhian N and Brooks, Jonah C and Gr{\"u}nwald, Niklaus J},
  journal={Name: Frontiers in Genetics},
  volume={6},
  url = {http://dx.doi.org/10.3389/fgene.2015.00208},
  doi = {10.3389/fgene.2015.00208},
  pages={208},
  year={2015}
}

@article{kamvar2015spatial,
  title={Spatial and temporal analysis of populations of the sudden oak death pathogen in Oregon forests},
  author={Kamvar, ZN and Larsen, MM and Kanaskie, AM and Hansen, EM and Gr{\"u}nwald, NJ},
  journal={Phytopathology},
  pages={PHYTO--12},
  year={2015},
  publisher={Am Phytopath Society},
  doi = {10.1094/PHYTO-12-14-0350-FI}
}

@article {bruvo2004simple,
  author = {Bruvo, R and Michiels, N K and D’Souza, T G and Schulenburg, H},
  title = {A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level},
  journal = {Molecular Ecology},
  volume = {13},
  number = {7},
  publisher = {Blackwell Science Ltd},
  issn = {1365-294X},
  url = {http://dx.doi.org/10.1111/j.1365-294X.2004.02209.x},
  doi = {10.1111/j.1365-294X.2004.02209.x},
  pages = {2101--2106},
  keywords = {microsatellites, parentage, polyploids, population, relatedness, Schmidtea},
  year = {2004},
}

@article{hedrick2005standardized,
  title={A standardized genetic differentiation measure},
  author={Hedrick, P W},
  journal={Evolution},
  volume={59},
  number={8},
  pages={1633--1638},
  year={2005},
  URL={http://dx.doi.org/10.1111/j.0014-3820.2005.tb01814.x},
  publisher={Wiley Online Library}
}

@article{meirmans2011assessing,
  title={{Assessing population structure: $F_{ST}$ and related measures}},
  author={Meirmans, P G and Hedrick, P W},
  journal={Molecular Ecology Resources},
  volume={11},
  number={1},
  pages={5--18},
  year={2011},
  publisher={Wiley Online Library},
  url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2010.02927.x/full}
}

@article{goss2009population,
  title={Population genetic analysis infers migration pathways of Phytophthora ramorum in US nurseries},
  author={Goss, Erica M and Larsen, Meg and Chastagner, Gary A and Givens, Donald R and Gr{\"u}nwald, Niklaus J},
  journal={PLoS Pathog},
  volume={5},
  number={9},
  pages={e1000583},
  year={2009}
}


@article{everhart2014finescale,
  title={Fine-scale genetic structure of {\textit{Monilinia fructicola}} during brown rot epidemics within individual peach tree canopies},
  author={Everhart, Sydney and Scherm, Harald},
  journal={Phytopathology},
  volume={105},
  number={4},
  pages={542--549},
  year={2015},
  publisher={Am Phytopath Society}
}

@article{goss2014irish,
author = {Goss, E M and Tabima, J F and Cooke, D E L and Restrepo, S and Fry, W E and Forbes, G A and Fieland, V J and Cardenas, M and Gr\"unwald, Niklaus J},
title = {The Irish potato famine pathogen \textit{{Phytophthora infestans}} originated in central Mexico rather than the Andes},
year = {2014},
volume = {111},
pages = {8791--8796},
doi = {10.1073/pnas.1401884111},
abstract ={Phytophthora infestans is a destructive plant pathogen best known for causing the disease that triggered the Irish potato famine and remains the most costly potato pathogen to manage worldwide. Identification of P. infestan’s elusive center of origin is critical to understanding the mechanisms of repeated global emergence of this pathogen. There are two competing theories, placing the origin in either South America or in central Mexico, both of which are centers of diversity of Solanum host plants. To test these competing hypotheses, we conducted detailed phylogeographic and approximate Bayesian computation analyses, which are suitable approaches to unraveling complex demographic histories. Our analyses used microsatellite markers and sequences of four nuclear genes sampled from populations in the Andes, Mexico, and elsewhere. To infer the ancestral state, we included the closest known relatives Phytophthora phaseoli, Phytophthora mirabilis, and Phytophthora ipomoeae, as well as the interspecific hybrid Phytophthora andina. We did not find support for an Andean origin of P. infestans; rather, the sequence data suggest a Mexican origin. Our findings support the hypothesis that populations found in the Andes are descendants of the Mexican populations and reconcile previous findings of ancestral variation in the Andes. Although centers of origin are well documented as centers of evolution and diversity for numerous crop plants, the number of plant pathogens with a known geographic origin are limited. This work has important implications for our understanding of the coevolution of hosts and pathogens, as well as the harnessing of plant disease resistance to manage late blight.},
URL = {http://www.pnas.org/content/early/2014/05/29/1401884111.abstract},
eprint = {http://www.pnas.org/content/early/2014/05/29/1401884111.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@article{pritchard2000inference,
  title={Inference of population structure using multilocus genotype data},
  author={Pritchard, J K and Stephens, M and Donnelly, P},
  journal={Genetics},
  volume={155},
  number={2},
  pages={945--959},
  year={2000},
  url = {http://www.genetics.org/content/155/2/945.abstract},
  publisher={Genetics Soc America}
}

@article{jombart2010discriminant,
  title={Discriminant analysis of principal components: a new method for the
    analysis of genetically structured populations},
  author={Jombart, T and Devillard, S and Balloux, F},
  journal={BMC genetics},
  volume={11},
  number={1},
  pages={94},
  year={2010},
  url = {http://www.biomedcentral.com/1471-2156/11/94},
  publisher={BioMed Central Ltd}
}

@article{kamvar2014poppr,
 title = {$Poppr$: an {R} package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction},
 author = {Kamvar, Z N and Tabima, J F and Gr\"unwald, Niklaus J},
 year = {2014},
 volume = {2},
 pages = {e281},
 journal = {PeerJ},
 url = {http://dx.doi.org/10.7717/peerj.281},
 doi = {10.7717/peerj.281}
}

@article{excoffier1992analysis,
  title={Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data},
  author={Excoffier, L and Smouse, P E and Quattro, J M},
  journal={Genetics},
  volume={131},
  number={2},
  pages={479--491},
  url = {http://www.genetics.org/content/131/2/479.abstract},
  year={1992},
  publisher={Genetics Soc America}
}

@book{ludwig1988statistical,
  title={Statistical ecology: a primer in methods and computing},
  author={Ludwig, J A and Reynolds, J F},
  year={1988},
  publisher={Wiley.com}
}

@book{pielou1975ecological,
  title={Ecological diversity},
  author={Pielou, E C},
  year={1975},
  publisher={Wiley New York}
}

@article{smith1993clonal,
  title={How clonal are bacteria},
  author={Smith, J M and Smith, N H and O'Rourke, M and Spratt, B G},
  journal={Proceedings of the National Academy of Sciences},
  volume={90},
  number={10},
  pages={4384--4388},
  url = {http://www.pnas.org/content/90/10/4384},
  year={1993},
  publisher={National Acad Sciences}
}

@article{brown1980multilocus,
  title={Multilocus structure of natural populations of \textit{{Hordeum spontaneum}}},
  author={Brown, A H D and Feldman, M W and Nevo, E},
  journal={Genetics},
  volume={96},
  number={2},
  pages={523--536},
  year={1980},
  url = {http://www.genetics.org/content/96/2/523},
  publisher={Genetics Soc America}
}

@article{agapow2001indices,
  title={Indices of multilocus linkage disequilibrium},
  author={Agapow, Paul-Michael and Burt, Austin},
  journal={Molecular Ecology Notes},
  volume={1},
  number={1-2},
  pages={101--102},
  year={2001},
  url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1471-8278.2000.00014.x/abstract},
  publisher={Wiley Online Library}
}

@article{nei1978estimation,
  title={Estimation of average heterozygosity and genetic distance from a small number of individuals},
  author={Nei, M},
  journal={Genetics},
  volume={89},
  number={3},
  pages={583--590},
  year={1978},
  url={http://www.genetics.org/content/89/3/583.abstract},
  publisher={Genetics Soc America}
}

@article{stoddart1988genotypic,
  title={Genotypic diversity: estimation and prediction in samples},
  author={Stoddart, J A and Taylor, J F},
  journal={Genetics},
  volume={118},
  number={4},
  pages={705--711},
  year={1988},
  url={http://www.genetics.org/content/118/4/705},
  publisher={Genetics Soc America}
}

@article{shannon2001mathematical,
  title={A mathematical theory of communication},
  author={Shannon, C E},
  journal={ACM SIGMOBILE Mobile Computing and Communications Review},
  volume={5},
  number={1},
  pages={3--55},
  year={2001},
  url={http://cm.bell-labs.com/cm/ms/what/shannonday/shannon1948.pdf},
  publisher={ACM}
}

@article{hurlbert1971nonconcept,
  title={The nonconcept of species diversity: a critique and alternative parameters},
  author={Hurlbert, S H},
  journal={Ecology},
  volume={52},
  number={4},
  pages={577--586},
  year={1971},
  url={http://www.jstor.org/discover/10.2307/1934145?uid=3739856&uid=2&uid=4&uid=3739256&sid=21103760010461},
  publisher={Eco Soc America}
}

@article{milgroom1996recombination,
  title={Recombination and the multilocus structure of fungal populations},
  author={Milgroom, M G},
  journal={Annual review of phytopathology},
  volume={34},
  number={1},
  pages={457--477},
  year={1996},
  url={http://www.annualreviews.org/doi/abs/10.1146/annurev.phyto.34.1.457},
  publisher={Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}
}

@article{balloux2003population,
  title={The population genetics of clonal and partially clonal diploids},
  author={Balloux, Fran{\c{c}}ois and Lehmann, Laurent and de Mee{\^u}s, Thierry},
  journal={Genetics},
  volume={164},
  number={4},
  pages={1635--1644},
  year={2003},
  url={http://www.genetics.org/content/164/4/1635.full},
  publisher={Genetics Soc America}
}

@article{de2006molecular,
  title={Molecular epidemiology of clonal diploids: a quick overview and a short DIY (do it yourself) notice},
  author={De Mee{\^u}s, T and Lehmann, L and Balloux, F},
  journal={Infection, Genetics and Evolution},
  volume={6},
  number={2},
  pages={163--170},
  year={2006},
  url={http://www.ncbi.nlm.nih.gov/pubmed/16290062},
  publisher={Elsevier}
}

@article{anderson1995clonality,
  title={Clonality in soilborne, plant-pathogenic fungi},
  author={Anderson, J B and Kohn, L M},
  journal={Annual Review of Phytopathology},
  volume={33},
  number={1},
  pages={369--391},
  year={1995},
  url={http://www.annualreviews.org/doi/abs/10.1146/annurev.py.33.090195.002101},
  publisher={Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}
}

@article{halkett2005tackling,
  title={Tackling the population genetics of clonal and partially clonal organisms},
  author={Halkett, F and Simon, J-C and Balloux, F},
  journal={Trends in Ecology \& Evolution},
  volume={20},
  number={4},
  pages={194--201},
  year={2005},
  url={http://www.ncbi.nlm.nih.gov/pubmed/16701368},
  publisher={Elsevier}
}

@article{grunwald2011evolution,
  title={Evolution and population genetics of exotic and re-emerging pathogens: Novel tools and approaches},
  author={Gr\"unwald, Niklaus J and Goss, Erica M},
  journal={Annual Review of Phytopathology},
  volume={49},
  pages={249--267},
  year={2011},
  url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-phyto-072910-095246?journalCode=phyto},
  publisher={Annual Reviews}
}

@article{linde2002population,
  title={Population structure of \textit{{Mycosphaerella graminicola}}: from lesions to continents},
  author={Linde, C C and Zhan, J and McDonald, B A},
  journal={Phytopathology},
  volume={92},
  number={9},
  pages={946--955},
  year={2002},
  url = {http://www.apsnet.org/edcenter/advanced/topics/PopGenetics/Documents/Linde.pdf},
  publisher={Am Phytopath Society}
}

@book{hein2004,
  title={Gene Genealogies, Variation and Evolution: A primer in coalescent theory},
  author={Hein, J and Schierup, M and Wiuf, C},
  isbn={9780191546150},
  lccn={2005295782},
  url={http://books.google.com/books?id=QBC\_SFOamksC},
  year={2004},
  publisher={Oxford University Press, USA}
}

@book{wakeley2009,
  title={Coalescent Theory: An Introduction},
  author={Wakeley, J},
  isbn={9780974707754},
  lccn={2008016081},
  url={http://books.google.com/books?id=x30RAgAACAAJ},
  year={2009},
  publisher={Roberts \& Company Publishers}
}

@book{weir1996,
  title={Genetic data analysis 2},
  author={Weir, BS},
  isbn={9780878939022},
  lccn={96017850},
  url={http://books.google.com/books?id=e9QPAQAAMAAJ},
  year={1996},
  publisher={Sinauer Associates}
}

@book{hartl2007,
  title={Principles of Population Genetics},
  author={Hartl, DL and Clark, AG},
  isbn={9780878933082},
  lccn={2006036153},
  url={http://books.google.com/books?id=SB1vQgAACAAJ},
  year={2007},
  publisher={Sinauer Associates, Incorporated}
}

@Manual{knitr2013,
  title = {$knitr$: A general-purpose package for dynamic report
  generation in R},
  author = {Alastair Andrew and Alex Zvoleff and Brian Diggs and
  Cassio Pereira and Hadley Wickham and Heewon Jeon and Jeff Arnold
  and Jeremy Stephens and Jim Hester and Joe Cheng and Jonathan
  Keane and J.J. Allaire and Johan Toloe and Kohske Takahashi and
  Michel Kuhlmann and Nacho Caballero and Nick Salkowski and Noam
  Ross and Ramnath Vaidyanathan and Richard Cotton and Romain
  Francois and Sietse Brouwer and Simon de Bernard and Taiyun Wei
  and Thibaut Lamadon and Tom Torsney-Weir and Trevor Davis and
  Weicheng Zhu and Wush Wu and Yihui Xie},
  year = {2013},
  note = {R package version 1.5},
  url = {http://yihui.name/knitr/},
}

@book{nielsen2013,
  title={An Introduction to Population Genetics: Theory and Applications},
  author={Nielsen, R and Slatkin, M},
  isbn={9781605351537},
  lccn={2012046169},
  url={http://books.google.com/books?id=Iy08kgEACAAJ},
  year={2013},
  publisher={Sinauer Associates, Incorporated}
}

@article{grunwald2006hierarchical,
  title={Hierarchical analysis of diversity, selfing, and genetic
    differentiation in populations of the oomycete \textit{{Aphanomyces euteiches}}},
  author={Gr\"unwald, Niklaus J and Hoheisel, G-A},
  journal={Phytopathology},
  volume={96},
  number={10},
  pages={1134--1141},
  year={2006},
  url={http://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-96-1134},
  publisher={Am Phytopath Society}
}

@article {grunwald2003,
  title = {Analysis of genotypic diversity data for populations of microorganisms},
  journal = {Phytopathology},
  volume = {93},
  number = {6},
  year = {2003},
  pages = {738--746},
  url={http://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO.2003.93.6.738},
  author = {Gr\"unwald, Niklaus J and Goodwin, Stephen B and Milgroom, Michael G and Fry, William E}
}

@article{laloe2007consensus,
    author = {Laloe, D and Jombart, T and Dufour, A-B and Moazami-Goudarzi, K},
    doi = {10.1051/gse:2007021},
    journal = {Genetics Selection Evolution},
    pages = {545--567},
    title = {Consensus genetic structuring and typological value of markers using multiple co-inertia analysis},
    url = {http://dx.doi.org/10.1051/gse:2007021},
    volume = {39},
    year = {2007}
}


@book{templeton2006,
  title={Population Genetics and Microevolutionary Theory},
  author={Templeton, AR},
  isbn={9780470047217},
  url={http://books.google.com/books?id=tJVreQjInt0C},
  year={2006},
  publisher={Wiley}
}

@book{felsenstein2004,
  title={Inferring Phylogenies},
  author={Felsenstein, J},
  isbn={9780878931774},
  lccn={2003008942},
  url={http://books.google.com/books?id=GI6PQgAACAAJ},
  year={2004},
  publisher={Sinauer Associates, Incorporated}
}


@article{Baird:2008cq,
author = {Baird, Nathan A and Etter, Paul D and Atwood, Tressa S and Currey, Mark C and Shiver, Anthony L and Lewis, Zachary A and Selker, Eric U and Cresko, William A and Johnson, Eric A},
title = {{Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers}},
journal = {PLoS ONE},
year = {2008},
volume = {3},
number = {10},
url={http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003376},
pages = {e3376},
month = oct
}

@article{ROWE:2011ks,
author = {Rowe, H C and Renaut, S and Guggisberg, A},
title = {{RAD in the realm of next-generation sequencing technologies}},
journal = {Molecular Ecology},
year = {2011},
volume = {20},
number = {17},
url={http://www.ncbi.nlm.nih.gov/pubmed/21991593},
pages = {3499--3502},
month = sep
}

@article{Poland:2012hs,
author = {Poland, Jesse and Endelman, Jeffrey and Dawson, Julie and Rutkoski, Jessica and Wu, Shuangye and Manes, Yann and Dreisigacker, Susanne and Crossa, Jos{\'e} and S{\'a}nchez-Villeda, H{\'e}ctor and Sorrells, Mark and Jannink, Jean-Luc},
title = {{Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing}},
journal = {The Plant Genome},
year = {2012},
volume = {5},
number = {3},
url={http://dl.sciencesocieties.org/publications/tpg/abstracts/5/3/103},
pages = {103--113},
month = nov
}


@article{tabachnick2001using,
  title={Using multivariate statistics},
  author={Tabachnick, Barbara G and Fidell, Linda S and Osterlind, Steven J},
  year={2001},
  publisher={Allyn and Bacon Boston}
}

@article{Tabima:InPrep,
author = {Tabima, J F and Zasada, I and Coffey, M and Gr\"unwald, Niklaus J},
title = {{Population dynamics of \testit{{P}hytopthora rubi} indicate high rates of migration between states and nurseries in the Pacific North Western {U}nited {S}tates}},
journal = {In prep},
year = {In Prep}
}

@article{mckenna2010genome,
  title={The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data},
  author={McKenna, Aaron and Hanna, Matthew and Banks, Eric and Sivachenko, Andrey and Cibulskis, Kristian and Kernytsky, Andrew and Garimella, Kiran and Altshuler, David and Gabriel, Stacey and Daly, Mark and others},
  journal={Genome research},
  volume={20},
  number={9},
  pages={1297--1303},
  year={2010},
  publisher={Cold Spring Harbor Lab}
}

@article{langmead2012fast,
  title={Fast gapped-read alignment with Bowtie 2},
  author={Langmead, Ben and Salzberg, Steven L},
  journal={Nature methods},
  volume={9},
  number={4},
  pages={357--359},
  year={2012},
  publisher={Nature Research}
}