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

 Package: msa

 Type: Package

 Title: Multiple Sequence Alignment

-Version: 1.17.1

-Date: 2019-09-12

+Version: 1.17.2

+Date: 2019-10-17

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

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

 Description: The 'msa' package provides a unified R/Bioconductor interface to

@@ -4,7 +4,10 @@ Change history of package msa:

 Version 1.18.0:

 - release as part of Bioconductor 3.10

-Version 1.7.1:

+Version 1.17.2:

+- removed change history from package vignette for easier maintenance

+

+Version 1.17.1:

 - fixed regular expression to comply with PCRE2

 - fixed Windows makefile for gc lib

 - fixed Windows cleanup script

@@ -6,12 +6,12 @@

 \hypersetup{colorlinks=false,

     pdfborder=0 0 0,

     pdftitle={msa - An R Package for Multiple Sequence Alignment},

-    pdfauthor={Enrico Bonatesta, Christoph Horejs-Kainrath, and Ulrich Bodenhofer}}

+    pdfauthor={Enrico Bonatesta, Christoph Kainrath, and Ulrich Bodenhofer}}

 \usepackage[OT1]{fontenc}

 \title{{\Huge msa}\\[5mm] An R Package for Multiple Sequence Alignment}

-\author{Enrico Bonatesta, Christoph Horej\v{s}-Kainrath, and Ulrich Bodenhofer}

+\author{Enrico Bonatesta, Christoph Kainrath, and Ulrich Bodenhofer}

 \affiliation{Institute of Bioinformatics, Johannes Kepler University

 Linz\\Altenberger Str. 69, 4040 Linz, Austria\\

 \email{msa@bioinf.jku.at}}

@@ -887,126 +887,6 @@ Moreover, we insist that, any time you cite the package, you also cite

 the original paper in which the original algorithm has been introduced (see

 bibliography below).

-\section{Change Log}

-

-\begin{description}

-\item[Version 1.18.0:] release as part of Bioconductor 3.10

-\item[Version 1.17.1:] \mbox{ }  \begin{itemize}

-   \item fixed regular expression to comply with PCRE2

-   \item fixed Windows makefile for gc lib

-   \item fixed Windows cleanup script

-   \item fixed\verb+ src/Makevars.win+

-  \end{itemize}

-\item[Version 1.17.0:] new branch for Bioconductor 3.10 devel

-\item[Version 1.16.0:] release as part of Bioconductor 3.9

-\item[Version 1.15.0:] new branch for Bioconductor 3.9 devel

-\item[Version 1.14.0:] release as part of Bioconductor 3.8

-\item[Version 1.13.0:] new branch for Bioconductor 3.8 devel

-\item[Version 1.12.0:] release as part of Bioconductor 3.7

-\item[Version 1.11.2:] \mbox{ }  \begin{itemize}

-   \item minor fix in ClustalW

-  \end{itemize}

-\item[Version 1.11.1:] \mbox{ }  \begin{itemize}

-   \item fix of code for using custom substitution matrices in ClustalW

-  \end{itemize}

-\item[Version 1.11.0:] new branch for Bioconductor 3.7 devel

-\item[Version 1.10.0:] release as part of Bioconductor 3.56

-\item[Version 1.9.0:] new branch for Bioconductor 3.6 devel

-\item[Version 1.8.0:] release as part of Bioconductor 3.5

-\item[Version 1.7.2:] \mbox{ }  \begin{itemize}

-   \item fix for new \verb+clang+ 4 compiler on Mac OS

-  \end{itemize}

-\item[Version 1.7.1:] \mbox{ }  \begin{itemize}

-   \item additional conversions implemented for \verb+msaConvert()+ function

-   \item added a new method \verb+msaConsensusSequence()+ that extends the

-     functionality provided by \verb+Biostring+'s \verb+consensusString()+ method

-   \item added a new method \verb+msaConservationScore()+

-   \item \verb+print()+ method extended such that it now also allows for

-     customization of the consensus sequence (via the new

-     \verb+msaConsensusSequence()+ method)

-   \item package now depends on \verb+Biostrings+ version $\geq$2.40.0 in order

-     to make sure that \verb+consensusMatrix()+ also works correctly

-     for masked alignments

-   \item corresponding changes in documentation and vignette

-  \end{itemize}

-\item[Version 1.7.0:] new branch for Bioconductor 3.5 devel

-\item[Version 1.6.0:] release as part of Bioconductor 3.4

-\item[Version 1.5.5:] \mbox{ }  \begin{itemize}

-   \item fixes in ClustalOmega source code to ensure Windows compatibility of

-   GCC6 compatibility fix

-   \end{itemize}

-\item[Version 1.5.4:] \mbox{ }  \begin{itemize}

-   \item bug fix in \verb+msaClustalW()+: unsupported parameter `\verb+tree+' deactivated

-   \item fixes in ClustalOmega source code to ensure GCC 6 compatibility

-   \item fix in \verb+msaConvert()+ function to improve safety of call to suggested

-  package \verb+phangorn+

-  \end{itemize}

-\item[Version 1.5.3:] \mbox{ }  \begin{itemize}

-   \item additional conversions implemented for \verb+msaConvert()+ function

-   \item corresponding changes in documentation

-  \end{itemize}

-\item[Versions 1.5.1 and 1.5.2:] version number bumps for technical reasons

-  related to Bioconductor build servers

-\item[Version 1.5.0:] new branch for Bioconductor 3.4 devel

-\item[Version 1.4.0:] release as part of Bioconductor 3.3

-\item[Version 1.3.7:] \mbox{ }  \begin{itemize}

-   \item fixes in \verb+msaPrettyPrint()+ function

-  \end{itemize}

-\item[Version 1.3.6:] \mbox) { }  \begin{itemize}

-   \item \verb+msaPrettyPrint()+ now also accepts dashes in file names

-   \item added section about pretty-printing wide alignments to package vignette

-  \end{itemize}

-\item[Version 1.3.5:] \mbox{ }  \begin{itemize}

-   \item adaptation of displaying help text by \verb+msa()+ function

-  \end{itemize}

-\item[Version 1.3.4:] \mbox{ }  \begin{itemize}

-   \item added function for checking and fixing sequence names for

-     possibly problematic characters that could lead to \LaTeX\ errors

-     when using \verb+msaPrettyPrint()+

-   \item corresponding changes in documentation

-   \item minor namespace fix

-  \end{itemize}

-\item[Version 1.3.3:] \mbox{ }  \begin{itemize}

-   \item added function for converting multiple sequence alignments for

-     use with other sequence alignment packages

-   \item corresponding changes in documentation

-  \end{itemize}

-\item[Version 1.3.2:] \mbox{ }  \begin{itemize}

-   \item further fixes in Makefiles and Makevars files to account for changes in build system

-   \item update of citation information

-  \end{itemize}

-\item[Version 1.3.1:] \mbox{ }  \begin{itemize}

-   \item fixes in Makefiles and Makevars files to account for changes in build system

-  \end{itemize}

-\item[Version 1.3.0:] new branch for Bioconductor 3.3 devel

-\item[Version 1.2.0:] release as part of Bioconductor 3.2

-\item[Version 1.1.3:] \mbox{ }  \begin{itemize}

-    \item bug fix related to custom substitution matrices

-      in the MUSCLE interface

-    \item corrections and updates of documentation

-  \end{itemize}

-\item[Version 1.1.2:] \mbox{ }  \begin{itemize}

-    \item new \verb+print()+ function for multiple alignments that also

-      allows for displaying alignments in their entirety (plus additional

-      customizations)

-    \item strongly improved handling of custom substitution matrices by

-      \verb+msaClustalW()+: now custom matrices can also be supplied for nucleotide

-      sequences which can also be passed via the \verb+substitutionMatrix+ argument.

-      The \verb+dnamatrix+ argument is still available for the sake of backwards

-      compatibility.

-    \item strongly improved handling of custom substitution matrices by

-      \verb+msaMuscle()+

-    \item fix of improperly aligned sequence logos produced by

-      \verb+msaPrettyPrint()+

-    \item updated citation information

-  \end{itemize}

-\item[Version 1.1.1:]  \mbox{ }  \begin{itemize}

-    \item fix of \verb+msa()+ function

-  \end{itemize}

-\item[Version 1.1.0:] new branch for Bioconductor 3.2 devel

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

-\end{description}

-

 \bibliographystyle{plain}

 \bibliography{lit}