references.bib

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@Manual{boettiger2014knitcitations,
  Title                    = {knitcitations: Citations for knitr markdown files},
  Author                   = {Carl Boettiger},
  Note                     = {R package version 1.0.5},
  Year                     = {2014},

  Url                      = {http://CRAN.R-project.org/package=knitcitations}
}

@Article{Fletcher2009,
  Title                    = {INDELible: a flexible simulator of biological sequence evolution.},
  Author                   = {Fletcher, William and Yang, Ziheng},
  Journal                  = {Mol Biol Evol},
  Year                     = {2009},

  Month                    = {Aug},
  Number                   = {8},
  Pages                    = {1879--1888},
  Volume                   = {26},

  __markedentry            = {[simon:6]},
  Abstract                 = {Many methods exist for reconstructing phylogenies from molecular sequence data, but few phylogenies are known and can be used to check their efficacy. Simulation remains the most important approach to testing the accuracy and robustness of phylogenetic inference methods. However, current simulation programs are limited, especially concerning realistic models for simulating insertions and deletions. We implement a portable and flexible application, named INDELible, for generating nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. Indels are simulated under several models of indel-length distribution. The program implements a rich repertoire of substitution models, including the general unrestricted model and nonstationary nonhomogeneous models of nucleotide substitution, mixture, and partition models that account for heterogeneity among sites, and codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and branches. With its many unique features, INDELible should be useful for evaluating the performance of many inference methods, including those for multiple sequence alignment, phylogenetic tree inference, and ancestral sequence, or genome reconstruction.},
  Doi                      = {10.1093/molbev/msp098},
  Institution              = {Department of Genetics, Evolution and Environment and Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, UK.},
  Keywords                 = {Algorithms; Animals; Evolution, Molecular; Humans; INDEL Mutation; Models, Genetic; Software},
  Language                 = {eng},
  Medline-pst              = {ppublish},
  Owner                    = {simon},
  Pii                      = {msp098},
  Pmid                     = {19423664},
  Timestamp                = {2015.05.25},
  Url                      = {http://dx.doi.org/10.1093/molbev/msp098}
}

@Manual{2014gitbook,
  Title                    = {Gitbook: Build beautiful interactive books using GitHub/Git and Markdown},
  Author                   = {Samy Pesse and Aaron O'Mullan},
  Year                     = {2014},

  Url                      = {http://www.gitbook.io/}
}

@Article{Ray2000,
  Title                    = {Genetic epidemiology of hepatitis C virus throughout egypt.},
  Author                   = {Ray, S. C. and Arthur, R. R. and Carella, A. and Bukh, J. and Thomas, D. L.},
  Journal                  = {J Infect Dis},
  Year                     = {2000},

  Month                    = {Sep},
  Number                   = {3},
  Pages                    = {698--707},
  Volume                   = {182},

  __markedentry            = {[simon:]},
  Abstract                 = {Hepatitis C virus (HCV) infection is a major health problem in Egypt, where the seroprevalence is 10-20-fold higher than that in the United States. To characterize the HCV genotype distribution and concordance of genotype assessments on the basis of multiple genomic regions, specimens were obtained from blood donors in 15 geographically diverse governorates throughout Egypt. The 5' noncoding, core/E1, and NS5B regions were amplified by reverse transcription-polymerase chain reaction and analyzed by both restriction fragment length polymorphism (RFLP) and phylogenetic tree construction. For the 5' noncoding region, 122 (64\%) of 190 specimens were amplified and analyzed by RFLP: 111 (91\%) were genotype 4, 1 (1\%) was genotype 1a, 1 (1\%) was genotype 1b, and 9 (7\%) could not be typed. Phylogenetic analyses of the core/E1 and NS5B regions confirmed the genotype 4 preponderance and revealed evidence of 3 new subtypes. Analysis of genetic distance between isolates was consistent with the introduction of multiple virus strains 75-140 years ago, and no clustering was detected within geographic regions, suggesting widespread dispersion at some time since then.},
  Doi                      = {10.1086/315786},
  Institution              = {Division of Infectious Diseases, Baltimore, MD 21205, USA. sray@jhmi. edu},
  Keywords                 = {Blood Donors; Egypt, epidemiology; Genotype; Hepacivirus, genetics; Hepatitis C, epidemiology/genetics; Humans; Phylogeny; Polymorphism, Restriction Fragment Length; RNA Replicase, genetics; Reverse Transcriptase Polymerase Chain Reaction; Seroepidemiologic Studies; Viral Envelope Proteins, genetics; Viral Nonstructural Proteins, genetics},
  Language                 = {eng},
  Medline-pst              = {ppublish},
  Owner                    = {simon},
  Pii                      = {JID000477},
  Pmid                     = {10950762},
  Timestamp                = {2015.05.22},
  Url                      = {http://dx.doi.org/10.1086/315786}
}

@Manual{wickham2015devtools,
  Title                    = {devtools: Tools to Make Developing R Packages Easier},
  Author                   = {Hadley Wickham and Winston Chang},
  Note                     = {R package version 1.7.0},
  Year                     = {2015},

  Url                      = {http://CRAN.R-project.org/package=devtools}
}

@Manual{xie2015knitr,
  Title                    = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
  Author                   = {Yihui Xie},
  Note                     = {R package version 1.10},
  Year                     = {2015},

  Url                      = {http://yihui.name/knitr/}
}