@article{Beitz2000,
  author =	 {E. Beitz},
  title =	 {{\TeX shade}: shading and labeling of multiple
                  sequence alignments using {\LaTeX2e}},
  journal =	 {Bioinformatics},
  year =	 2000,
  volume =	 16,
  number =	 2,
  pages =	 {135--139}
}

@incollection{CharifLobry2007,
  author =	 {D. Charif and J. R. Lobry},
  title =	 {Seqin{R} 1.0-2: a contributed package to the {R}
                  project for statistical computing devoted to
                  biological sequences retrieval and analysis},
  booktitle =	 {Structural approaches to sequence evolution:
                  Molecules, networks, populations},
  year =	 2007,
  editor =	 {U. Bastolla and M. Porto and H. E. Roman and
                  M. Vendruscolo},
  series =	 {Biological and Medical Physics, Biomedical
                  Engineering},
  pages =	 {207--232},
  address =	 {New York},
  publisher =	 {Springer}
}

@article{Eddelbuettel2011,
  title =	 {{Rcpp}: Seamless {R} and {C++} Integration},
  author =	 {D. Eddelbuettel and R. Fran\c{c}ois},
  journal =	 {Journal of Statistical Software},
  year =	 2011,
  volume =	 40,
  number =	 8,
  pages =	 {1--18}
}

@book{Eddelbuettel2013,
  title =	 {Seamless {R} and {C++} Integration with {Rcpp}},
  author =	 {D. Eddelbuettel},
  publisher =	 {Springer},
  address =	 {New York},
  year =	 2013
}

@article{Edgar2004a,
  author =	 {R. C. Edgar},
  title =	 {{MUSCLE:} multiple sequence alignment with high
                  accuracy and high throughput},
  journal =	 {Nucleic Acids Res.},
  year =	 2004,
  volume =	 32,
  number =	 5,
  pages =	 {1792--1797}
}

@article{Edgar2004b,
  author =	 {R. C. Edgar},
  title =	 {{MUSCLE}: a multiple sequence alignment method with
                  reduced time and space complexity},
  journal =	 {BMC Bioinformatics},
  number =	 5,
  pages =	 113,
  volume =	 5,
  year =	 2004
}

@book{Lamport1999,
  title =	 {{\LaTeX} --- A Document Preparation System. User's
                  Guide and Reference Manual},
  author =	 {L. Lamport},
  publisher =	 {Addison-Wesley Longman},
  address =	 {Amsterdam},
  year =	 1999
}

@inproceedings{Leisch2002,
  author =	 {F. Leisch},
  title =	 {Sweave: dynamic generation of statistical reports
                  using literate data analysis},
  editor =	 {W. H\"ardle and B. R\"onz},
  booktitle =	 {Compstat 2002 --- Proceedings in Computational
                  Statistics},
  publisher =	 {Physica-Verlag},
  address =	 {Heidelberg},
  pages =	 {575--580},
  year =	 2002
}

@article{Morgenstern1999,
  author =	 {B. Morgenstern},
  title =	 {{DIALIGN 2}: improvement of the segment-to-segment
                  approach to multiple sequence alignment},
  journal =	 {Bioinformatics},
  year =	 1999,
  volume =	 15,
  number =	 3,
  pages =	 {211--218}
}

@inproceedings{Nethercote2007,
  author =	 {N. Nethercote and J. Seward},
  title =	 {Valgrind: A Framework for Heavyweight Dynamic Binary
                  Instrumentation},
  booktitle =	 {Proc. of the ACM SIGPLAN 2007 Conf. on Programming
                  Language Design and Implementation},
  address =	 {San Diego, CA},
  year =	 2007
}

@article{Notredame2000,
  author =	 {C. Notredame and D. G. Higgins and J. Heringa},
  title =	 {{T-Coffee}: A novel method for fast and accurate
                  multiple sequence alignment},
  journal =	 {J. Mol. Biol.},
  year =	 2000,
  volume =	 302,
  number =	 1,
  pages =	 {205--217}
}

@article{ParadisClaudeStrimmer2004,
  title =	 {A{PE}: analyses of phylogenetics and evolution in
                  {R} language},
  author =	 {E. Paradis and J. Claude and K. Strimmer},
  journal =	 {Bioinformatics},
  year =	 2004,
  volume =	 20,
  pages =	 {289--290},
}

@manual{PeleBecuAbdiChabbert2012,
  title =	 {{bios2mds: From BIOlogical Sequences to
                  MultiDimensional Scaling}},
  author =	 {J. Pele with J.-M. Becu and H. Abdi and
                  M. Chabbert},
  year =	 2012,
  note =	 {R package version 1.2.2}
}

@article{Schliep2011,
  title =	 {phangorn: phylogenetic analysis in {R}},
  author =	 {K. P. Schliep},
  journal =	 {Bioinformatics},
  year =	 2011,
  volume =	 27,
  number =	 4,
  pages =	 {592--593},
}

@article{Sievers2011,
  author =	 {F. Sievers and A. Wilm and D. Dineen and
                  T. J. Gibson and K. Karplus and W. Li and R. Lopez
                  and H. McWilliam and M. Remmert and J. S\"oding and
                  J. D. Thompson and D. G. Higgins},
  title =	 {Fast, scalable generation of high-quality protein
                  multiple sequence alignments using {Clustal Omega}},
  journal =	 {Mol. Syst. Biol.},
  volume =	 7,
  pages =	 539,
  year =	 2011
}

@article{Thompson1994,
  author =	 {J. D. Thompson and D. G. Higgins and T. J. Gibson},
  title =	 {{CLUSTAL W}: improving the sensitivity of
                  progressive multiple sequence alignment through
                  sequence weighting, position-specific gap penalties
                  and weight matrix choice.},
  journal =	 {Nucleic Acids Res.},
  year =	 2004,
  volume =	 22,
  number =	 22,
  pages =	 {4673--4680}
}

@book{Xie2014,
  title =	 {Dynamic Documents with R and knitr},
  author =	 {Y. Xie},
  publisher =	 {Chapman \&\ Hall/CRC},
  year =	 2014
}

@article{YuSmithZhuGuanLam2016,
  title =	 {ggtree: an {R} package for visualization and
                  annotation of phylogenetic tree with different types
                  of meta-data},
  author =	 {G. Yu and D. Smith and H. Zhu and Y. Guan and
                  T. T. Y. Lam},
  year =	 {submitted}
}
