Change history of package msa:
==============================

Version 1.3.4:
- added function for checking and fixing sequence names for
  possibly problematic characters that could lead to LaTeX
  errors when using msaPrettyPrint()
- corresponding changes in documentation
- minor namespace fix

Version 1.3.3:
- added function for converting multiple sequence alignments for
  use with other sequence alignment packages
- corresponding changes in documentation

Version 1.3.2:
- further fixes in Makefiles and Makevars files to account for changes
  in build system
- update of citation information

Version 1.3.1:
- fixes in Makefiles and Makevars files to account for changes in build system

Version 1.3.0:
- new branch for Bioconductor 3.3 devel

Version 1.1.3: 
- bug fix related to custom substitution matrices in the MUSCLE interface
- correction and updates of documentation

Version 1.1.2:
- new print() function for multiple alignments that also
  allows for displaying alignments in their entirety (plus additional
  customizations)
- strongly improved handling of custom substitution matrices by
  msaClustalW(): now custom matrices can also be supplied for nucleotide
  sequences which can also be passed via the 'substitutionMatrix' argument.
  The 'dnamatrix' argument is still available for the sake of backwards
  compatibility.
- strongly improved handling of custom substitution matrices by
  msaMuscle()
- fix of improperly aligned sequence logos produced by msaPrettyPrint()
- updated citation information

Version 1.1.1:
- fix of msa() function

Version 1.1.0:
- new branch for Bioconductor 3.2 devel

Version 1.0.0:
- first official release as part of Bioconductor 3.1