@@ -9,6 +9,23 @@

   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},

@@ -103,6 +120,35 @@

   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

@@ -135,3 +181,12 @@

   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}

+}

new file mode 100644

@@ -0,0 +1,137 @@

+@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}

+}

+

+@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{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

+}