@@ -1,8 +1,8 @@

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.0.1

-Date: 2015-06-12

+Version: 1.0.2

+Date: 2015-09-29

 Author: Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer

 Maintainer: Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>

 Description: This package provides a unified R/Bioconductor interface to the

@@ -57,24 +57,24 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

         stop("The parameter alFile has an invalid argument!")

     if (!is(x, "MultipleAlignment"))

-        stop("The parameter x has an invalid argument! \n", 

+        stop("The parameter x has an invalid argument! \n",

              "x must be a multiple alignment object!")

-    

+

     if (output != "asis")

     {

         if (!is.numeric(paperWidth) || length(paperWidth) != 1 ||

             paperWidth <= 0)

-            stop("The parameter paperWidth must be ", 

+            stop("The parameter paperWidth must be ",

                  "single positive number (unit: inches)!")

         if (!is.numeric(paperHeight) || length(paperHeight) != 1 ||

             paperHeight <= 0)

-            stop("The parameter paperHeight must be ", 

+            stop("The parameter paperHeight must be ",

                  "single positive number (unit: inches)!")

         if (!is.numeric(margins) || length(margins) != 2)

-            stop("The parameter margins must be ", 

+            stop("The parameter margins must be ",

                  "two positive numbers (unit: inches)!")

     }

@@ -85,14 +85,14 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

             if (max(subset) < .Machine$integer.max)

                 subset <- as.integer(subset)

             else

-               stop("One or more values for parameter subset ", 

+               stop("One or more values for parameter subset ",

                     "are larger than integer!")

         }

         else if (!is.integer(subset))

             stop("The parameter subset has an invalid argument!")

         if (length(subset) < 2)

-            stop("The parameter subset is expected to be \n", 

+            stop("The parameter subset is expected to be \n",

                  " a vector with at least 2 entries!")

         if (!all(subset %in% 1:nrow(x)))

@@ -122,7 +122,7 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

     if (!is.numeric(consensusThreshold) || length(consensusThreshold) != 1 ||

         consensusThreshold < 0 || consensusThreshold > 100)

-        stop("The parameter consensusThreshold must be \n", 

+        stop("The parameter consensusThreshold must be \n",

              "a single numeric between 0 and 100 !")

     if (shadingMode %in% c("identical", "similar"))

@@ -151,9 +151,9 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

                                          "accessible area"))

         else

             stop("Missing shadingModeArg for functional shading mode. \n",

-                 "Valid values are: \n", 

-                 "\"charge\", \n", 

-                 "\"hydropathy\", \n", 

+                 "Valid values are: \n",

+                 "\"charge\", \n",

+                 "\"hydropathy\", \n",

                  "\"structure\", \n",

                  "\"chemical\",\n",

                  " \"rasmol\",\n",

@@ -203,7 +203,7 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

     if (output != "asis")

     {

         if (!is.character(file) || length(file) > 1)

-            stop("The argument for parameter file must be \n", 

+            stop("The argument for parameter file must be \n",

                  "a single character string!")

         if (substr(file, nchar(file) - 2, nchar(file)) != output)

@@ -241,6 +241,11 @@ msaPrettyPrint <- function(x, y, output=c("pdf", "tex", "dvi", "asis"),

     texOutput <- paste0("\\begin{texshade}{", stratifyFilenames(alFile), "}")

+    if (is(x, "AAMultipleAlignment"))

+        texOutput <- c(texOutput, "\\seqtype{P}")

+    else

+        texOutput <- c(texOutput, "\\seqtype{N}")

+

     if (length(toShow) == 1)

     {

         if (sum(width(toShow)) < ncol(x))

@@ -1,7 +1,7 @@

 ##345678901234567890123456789012345678901234567890123456789012345678901234567890

 citHeader("To cite package 'msa' in publications use:")

-#year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl = TRUE) 

+#year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl = TRUE)

 #vers <- paste("R package version", meta$Version)

 desc <- packageDescription("msa")

 year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", desc$Date)

@@ -9,19 +9,21 @@ vers <- paste("R package version", desc$Version)

 url  <- desc$URL

-citEntry(entry="Manual", 

-         title = "msa -- An R Package for Multiple Sequence Alignment.", 

-         author = personList(as.person("Enrico Bonatesta"), as.person("Christoph Horejs-Kainrath"), as.person("Ulrich Bodenhofer")),

-         year = year, 

-         note = vers,

-         organization=paste("Institute of Bioinformatics",

-                            "Johannes Kepler University", sep=", "),

-         address="Linz, Austria",

-         url=url,

-         textVersion = 

-             paste("Enrico Bonatesta, Christoph Horejs-Kainrath and Ulrich Bodenhofer (", year, "). ",

-                   "msa -- An R Package for Multiple Sequence Alignment. ",

-                   vers, ".", sep="")

+citEntry(entry="Article",

+         title = "msa: an R package for multiple sequence alignment",

+         author = personList(as.person("Ulrich Bodenhofer"),

+                             as.person("Enrico Bonatesta"),

+                             as.person("Christoph Horejs-Kainrath"),

+                             as.person("Sepp Hochreiter")),

+         journal="Bioinformatics",

+         note="(accepted)",

+         year="2015",

+         doi="10.1093/bioinformatics/btv494",

+         textVersion =

+             paste("U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015)",

+                   "msa: an R package for multiple sequence alignment.",

+                   "Bioinformatics (accepted).",

+                   "DOI: 10.1093/bioinformatics/btv176.")

 )

 citFooter(

@@ -1,6 +1,10 @@

 Change history of package msa:

 ==============================

+Version 1.0.2:

+- fix of improperly aligned sequence logos produced by msaPrettyPrint()

+- updated citation information

+

 Version 1.0.1:

 - fix of msa() function

@@ -37,6 +37,14 @@ The following slots are defined for \code{MsaMetaData} objects:

 \author{Enrico Bonatesta and Christoph Horejs-Kainrath

   <msa@bioinf.jku.at>

 }

+\references{

+  \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

+}

 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},

   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},

   \code{\linkS4class{MsaAAMultipleAlignment}},

@@ -81,6 +81,14 @@

 \author{Enrico Bonatesta and Christoph Horejs-Kainrath

   <msa@bioinf.jku.at>

 }

+\references{

+  \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

+}

 \seealso{\code{\link{msa}}, \code{\link{msaClustalW}},

   \code{\link{msaClustalOmega}}, \code{\link{msaMuscle}},

   \code{\linkS4class{MsaMetaData}}

@@ -27,6 +27,11 @@

 }

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)

   CLUSTAL W: improving the sensitivity of progressive multiple sequence

@@ -132,6 +132,11 @@

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

+ 

   \url{http://www.clustal.org/download/clustalw_help.txt}

   \url{http://www.clustal.org/omega/README}

@@ -76,6 +76,11 @@

 }

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   \url{http://www.clustal.org/omega/README}

@@ -79,7 +79,12 @@

 }

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

-  

+   

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

+ 

   \url{http://www.clustal.org/download/clustalw_help.txt}

   Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)

@@ -85,6 +85,11 @@

 }

 \references{

   \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

   \url{http://www.drive5.com/muscle/muscle.html}

@@ -188,9 +188,14 @@

   <msa@bioinf.jku.at>

 }

 \references{

-\url{http://www.bioinf.jku.at/software/msa}

+  \url{http://www.bioinf.jku.at/software/msa}

+  

+  U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter

+  (2015). msa: an R package for multiple sequence alignment. 

+  \emph{Bioinformatics} (accepted). DOI:

+  \href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

-\url{https://www.ctan.org/pkg/texshade}

+  \url{https://www.ctan.org/pkg/texshade}

   Beitz, E. (2000) TeXshade: shading and labeling of multiple

   sequence alignments using LaTeX2e

@@ -9,6 +9,38 @@

   pages =	 {135--139}

 }

+@article{Bodenhofer2015,

+  author =	 {U. Bodenhofer and E. Bonatesta and

+                  C. Horej\v{s}-Kainrath and S. Hochreiter},

+  title =	 {{msa}: an {R} package for multiple sequence

+                  alignment},

+  journal =	 {Bioinformatics},

+  year =	 2015,

+  note =	 {(accepted)}

+}

+

+@article{Brudno2003,

+  author =	 {M. Brudno and M. Chapman and B. G\"ottgens and

+                  S. Batzoglou and B. Morgenstern},

+  title =	 {Fast and sensitive multiple alignment of large

+                  genomic sequences},

+  journal =	 {BMC Bioinformatics},

+  year =	 2003,

+  volume =	 4,

+  pages =	 66

+}

+

+@article{Dagum1998,

+  author =	 {L. Dagum and R. Menon},

+  title =	 {{OpenMP}: an industry standard {API} for

+                  shared-memory programming},

+  journal =	 {Computational Science \&\ Engineering, IEEE},

+  volume =	 5,

+  number =	 1,

+  pages =	 {46--55},

+  year =	 1998

+}

+

 @article{Eddelbuettel2011,

   title =	 {{Rcpp}: Seamless {R} and {C++} Integration},

   author =	 {D. Eddelbuettel and R. Fran\c{c}ois},

@@ -49,6 +81,16 @@

   year =	 2004

 }

+@article{Edgar2006,

+  author =	 {R. C. Edgar and S. Batzoglou},

+  title =	 {Multiple sequence alignment},

+  journal =	 {Curr. Opin. Struct. Biol.},

+  volume =	 16,

+  number =	 3,

+  pages =	 {368--373},

+  year =	 2006

+}

+

 @book{Lamport1999,

   title =	 {{\LaTeX} --- A Document Preparation System. User's

                   Guide and Reference Manual},

@@ -58,6 +100,20 @@

   year =	 1999

 }

+@article{Larkin2007,

+  author =	 {M. A. Larkin and G. Blackshields and N. P. Brown and

+                  R. Chenna and P. A. McGettigan and H. McWilliam and

+                  F. Valentin and I. M. Wallace and A. Wilm and

+                  R. Lopez and J. D. Thompson and T. J. Gibson and

+                  D. G. Higgins},

+  title =	 {{Clustal W} and {Clustal X} version 2.0},

+  journal =	 {Bioinformatics},

+  year =	 2007,

+  volume =	 23,

+  number =	 21,

+  pages =	 {2947--2948}

+}

+

 @inproceedings{Leisch2002,

   author =	 {F. Leisch},

   title =	 {Sweave: dynamic generation of statistical reports

@@ -71,6 +127,17 @@

   year =	 2002

 }

+@article{Loytynoja2012,

+  author =	 {A. L\"oytynoja and A. J. Vilella and N. Goldman},

+  title =	 {Accurate extension of multiple sequence alignments

+                  using a phylogeny-aware graph algorithm},

+  journal =	 {Bioinformatics},

+  year =	 2012,

+  volume =	 28,

+  number =	 13,

+  pages =	 {1684--1691}

+}

+

 @article{Morgenstern1999,

   author =	 {B. Morgenstern},

   title =	 {{DIALIGN 2}: improvement of the segment-to-segment

@@ -103,6 +170,26 @@

   pages =	 {205--217}

 }

+@article{Notredame2007,

+  author =	 {C. Notredame},

+  title =	 {Recent Evolutions of Multiple Sequence Alignment

+                  Algorithms},

+  journal =	 {PLoS Comput. Biol.},

+  year =	 2007,

+  volume =	 3,

+  number =	 8,

+  pages =	 {e123}

+}

+

+@manual{Pages2015,

+  title =	 {Biostrings: String objects representing biological

+                  sequences, and matching algorithms},

+  author =	 {H. Pag\`es and P. Aboyoun and R. Gentleman and

+                  S. DebRoy},

+  note =	 {R package version 2.36.1},

+  year =	 2015

+}

+

 @article{Sievers2011,

   author =	 {F. Sievers and A. Wilm and D. Dineen and

                   T. J. Gibson and K. Karplus and W. Li and R. Lopez

@@ -116,6 +203,16 @@

   year =	 2011

 }

+@article{Szalkowski2012,

+  author =	 {A. M. Szalkowski},

+  title =	 {Fast and robust multiple sequence alignment with

+                  phylogeny-aware gap placement},

+  journal =	 {BMC Bioinformatics},

+  year =	 2012,

+  volume =	 13,

+  pages =	 129

+}

+

 @article{Thompson1994,

   author =	 {J. D. Thompson and D. G. Higgins and T. J. Gibson},

   title =	 {{CLUSTAL W}: improving the sensitivity of

@@ -129,6 +226,16 @@

   pages =	 {4673--4680}

 }

+@article{Wallace2005,

+  author =	 {I. M. Wallace and G. Blackshields and D. G. Higgins},

+  title =	 {Multiple sequence alignments},

+  journal =	 {Curr. Opin. Struct. Biol.},

+  volume =	 15,

+  number =	 3,

+  pages =	 {261--266},

+  year =	 2005

+}

+

 @book{Xie2014,

   title =	 {Dynamic Documents with R and knitr},

   author =	 {Y. Xie},

@@ -83,15 +83,16 @@ first have to read introductory literature on the subjects mentioned above.

 \section{Introduction}

 Multiple sequence alignment is one of the most fundamental tasks in

-bioinformatics. Algorithms like ClustalW~\cite{Thompson1994},

+bioinformatics. Algorithms like ClustalW~\cite{Thompson1994,Larkin2007},

 ClustalOmega~\cite{Sievers2011}, and MUSCLE~\cite{Edgar2004b,Edgar2004a}

-are well known and

-widely used. However, all these algorithms are implemented as stand-alone

+are well known and widely used (for more comprehensive overviews of methods,

+see \cite{Edgar2006,Notredame2007,Wallace2005}).

+However, all these algorithms are implemented as stand-alone

 commmand line programs without any integration into the R/Bioconductor

 ecosystem. Before the \MSA\ package, only the \verb+muscle+ package has

 been available in \R, but no other multiple sequence alignment algorithm,

 although the \verb+Biostrings+ package has provided data types for

-representing multiple sequence alignments for quite some time.

+representing multiple sequence alignments for quite some time \cite{Pages2015}.

 The \MSA\ package aims to close that gap by

 providing a unified R interface to the multiple sequence alignment algorithms

 ClustalW, ClustalOmega, and MUSCLE. The package requires no additional

@@ -541,12 +542,6 @@ has a minor memory leak, but the loss of data is so small that no major

 problems are to be expected except for thousands of executions of

 ClustalOmega.

-\subsubsection*{\shade: Alignment of Sequence Logos}

-

-\shade\ has some issues with aligning the sequence logo to the multiple

-sequence alignment. Under which conditions this happens, would require a

-more detailed investigation.

-

 \subsubsection*{ClustalOmega vs.\ Older GCC Versions on Linux/Unix}

 We have encountered peculiar behavior of ClustalOmega if the package was

@@ -562,7 +557,7 @@ to update to a newer GCC version and re-install the package.

 \subsubsection*{ClustalOmega: OpenMP Support on Mac OS}

 ClustalOmega is implemented to make use of OpenMP (if available on the

-target platform). Due to issues on one of the Bioconductor build servers

+target platform) \cite{Dagum1998}. Due to issues on one of the Bioconductor build servers

 running Mac OS, we had to deactivate OpenMP generally for Mac OS platforms.

 If a Mac OS user wants to re-activate OpenMP, he/she should download the

 source package tarball, untar it, comment/uncomment the corresponding line in

@@ -580,7 +575,8 @@ function. This interface will be improved in future versions.

 We envision the following changes/extensions in future versions of the package:

 \begin{itemize}

   \item Integration of more multiple sequence alignment algorithms, such as,

-    T-Coffee \cite{Notredame2000} or DIALIGN \cite{Morgenstern1999}

+    T-Coffee \cite{Notredame2000} or others

+    \cite{Brudno2003,Loytynoja2012,Morgenstern1999,Szalkowski2012}

   \item Support for retrieving guide trees from the multiple sequence

     alignment algorithms

   \item Interface to methods computing phylogenetic trees (e.g.\ as

@@ -595,10 +591,12 @@ We envision the following changes/extensions in future versions of the package:

 \section{How to Cite This Package}

 If you use this package for research that is published later, you are kindly

-asked to cite it as follows:

+asked to cite it as follows \cite{Bodenhofer2015}:

 \begin{quotation}

-\noindent E.~Bonatesta, C.~Horejs-Kainrath, and U.~Bodenhofer, (2015).

-msa: An R Package for Multiple Sequence Alignment.

+\noindent U.~Bodenhofer, E.~Bonatesta, C.~Horej\v{s}-Kainrath, and Sepp Hochreiter(2015).

+msa: an R Package for multiple sequence alignment.

+{\em Bioinformatics} (accepted). DOI:

+\href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

 \end{quotation}

 To obtain a Bib\TeX\ entries of the reference, enter the

 following into your R session:

@@ -613,6 +611,11 @@ bibliography below).

 \section{Change Log}

 \begin{description}

+\item[Version 1.0.2:] \mbox{ } \newline

+  \begin{itemize}

+    \item fix of improperly aligned sequence logos produced by \verb+msaPrettyPrint()+

+    \item updated citation information

+  \end{itemize}

 \item[Version 1.0.1:] fix of \verb+msa()+ function

 \item[Version 1.0.0:] first official release as part of Bioconductor 3.1

 \end{description}

@@ -628,6 +631,22 @@ E.~Beitz.

   using {\LaTeX2e}.

 \newblock {\em Bioinformatics}, 16(2):135--139, 2000.

+\bibitem{Bodenhofer2015}

+U.~Bodenhofer, E.~Bonatesta, C.~Horej\v{s}-Kainrath, and S.~Hochreiter.

+\newblock {msa}: an {R} package for multiple sequence alignment.

+\newblock {\em Bioinformatics}, 2015.

+\newblock (accepted).

+

+\bibitem{Brudno2003}

+M.~Brudno, M.~Chapman, B.~G\"ottgens, S.~Batzoglou, and B.~Morgenstern.

+\newblock Fast and sensitive multiple alignment of large genomic sequences.

+\newblock {\em BMC Bioinformatics}, 4:66, 2003.

+

+\bibitem{Dagum1998}

+L.~Dagum and R.~Menon.

+\newblock {OpenMP}: an industry standard {API} for shared-memory programming.

+\newblock {\em Computational Science \&\ Engineering, IEEE}, 5(1):46--55, 1998.

+

 \bibitem{Edgar2004b}

 R.~C. Edgar.

 \newblock {MUSCLE}: a multiple sequence alignment method with reduced time and

@@ -640,12 +659,24 @@ R.~C. Edgar.

   throughput.

 \newblock {\em Nucleic Acids Res.}, 32(5):1792--1797, 2004.

+\bibitem{Edgar2006}

+R.~C. Edgar and S.~Batzoglou.

+\newblock Multiple sequence alignment.

+\newblock {\em Curr. Opin. Struct. Biol.}, 16(3):368--373, 2006.

+

 \bibitem{Lamport1999}

 L.~Lamport.

 \newblock {\em {\LaTeX} --- A Document Preparation System. User's Guide and

   Reference Manual}.

 \newblock Addison-Wesley Longman, Amsterdam, 1999.

+\bibitem{Larkin2007}

+M.~A. Larkin, G.~Blackshields, N.~P. Brown, R.~Chenna, P.~A. McGettigan,

+  H.~McWilliam, F.~Valentin, I.~M. Wallace, A.~Wilm, R.~Lopez, J.~D. Thompson,

+  T.~J. Gibson, and D.~G. Higgins.

+\newblock {Clustal W} and {Clustal X} version 2.0.

+\newblock {\em Bioinformatics}, 23(21):2947--2948, 2007.

+

 \bibitem{Leisch2002}

 F.~Leisch.

 \newblock Sweave: dynamic generation of statistical reports using literate data

@@ -654,6 +685,12 @@ F.~Leisch.

   Proceedings in Computational Statistics}, pages 575--580, Heidelberg, 2002.

   Physica-Verlag.

+\bibitem{Loytynoja2012}

+A.~L\"oytynoja, A.~J. Vilella, and N.~Goldman.

+\newblock Accurate extension of multiple sequence alignments using a

+  phylogeny-aware graph algorithm.

+\newblock {\em Bioinformatics}, 28(13):1684--1691, 2012.

+

 \bibitem{Morgenstern1999}

 B.~Morgenstern.

 \newblock {DIALIGN 2}: improvement of the segment-to-segment approach to

@@ -666,12 +703,23 @@ N.~Nethercote and J.~Seward.

 \newblock In {\em Proc. of the ACM SIGPLAN 2007 Conf. on Programming Language

   Design and Implementation}, San Diego, CA, 2007.

+\bibitem{Notredame2007}

+C.~Notredame.

+\newblock Recent evolutions of multiple sequence alignment algorithms.

+\newblock {\em PLoS Comput. Biol.}, 3(8):e123, 2007.

+

 \bibitem{Notredame2000}

 C.~Notredame, D.~G. Higgins, and J.~Heringa.

 \newblock {T-Coffee}: A novel method for fast and accurate multiple sequence

   alignment.

 \newblock {\em J. Mol. Biol.}, 302(1):205--217, 2000.

+\bibitem{Pages2015}

+H.~Pag\`es, P.~Aboyoun, R.~Gentleman, and S.~DebRoy.

+\newblock {\em Biostrings: String objects representing biological sequences,

+  and matching algorithms}, 2015.

+\newblock R package version 2.36.1.

+

 \bibitem{Sievers2011}

 F.~Sievers, A.~Wilm, D.~Dineen, T.~J. Gibson, K.~Karplus, W.~Li, R.~Lopez,

   H.~McWilliam, M.~Remmert, J.~S\"oding, J.~D. Thompson, and D.~G. Higgins.

@@ -679,6 +727,12 @@ F.~Sievers, A.~Wilm, D.~Dineen, T.~J. Gibson, K.~Karplus, W.~Li, R.~Lopez,

   alignments using {Clustal Omega}.

 \newblock {\em Mol. Syst. Biol.}, 7:539, 2011.

+\bibitem{Szalkowski2012}

+A.~M. Szalkowski.

+\newblock Fast and robust multiple sequence alignment with phylogeny-aware gap

+  placement.

+\newblock {\em BMC Bioinformatics}, 13:129, 2012.

+

 \bibitem{Thompson1994}

 J.~D. Thompson, D.~G. Higgins, and T.~J. Gibson.

 \newblock {CLUSTAL W}: improving the sensitivity of progressive multiple

@@ -686,6 +740,11 @@ J.~D. Thompson, D.~G. Higgins, and T.~J. Gibson.

   penalties and weight matrix choice.

 \newblock {\em Nucleic Acids Res.}, 22(22):4673--4680, 2004.

+\bibitem{Wallace2005}

+I.~M. Wallace, G.~Blackshields, and D.~G. Higgins.

+\newblock Multiple sequence alignments.

+\newblock {\em Curr. Opin. Struct. Biol.}, 15(3):261--266, 2005.

+

 \bibitem{Xie2014}

 Y.~Xie.

 \newblock {\em Dynamic Documents with R and knitr}.