@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}
 }