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

The following list highlights the change history of the package.
It only mentions versions in which actual changes have been made
(leaving out automatic version number increments that have been made
within the Bioconductor release cycle without any actual change
of code or documentation).

Version 1.45.1:
- adapted imports to new MultipleAlignment package (Bioconductor 3.24)
- minor fix of link in help page

Version 1.43.1:
- fix of bug that deleted sequence names if the sequences were read from
  FASTA file (all three alignment algorithms)

Version 1.41.3:
- fix in ClustalOmega to better determine whether OpenMP is available
- updated DESCRIPTION file to new format (Authors@R)

Version 1.41.2:
- fix of memory leaks in Muscle (thanks for GitHub user Rong-Zh)

Version 1.41.1:
- fix of compilation issues caused by ClustalOmega on arm64 systems 

Version 1.39.5:
- workaround to avoid segfault caused by ClustalOmega 

Version 1.39.4:
- fix of gc 8.2.8 source for Windows platform

Version 1.39.3:
- upgraded gc library to version 8.2.8
- changed compiler standard to gnu++11 for ClustalOmega compilation on Linux/Mac
- fixed a bug regarding passing file names as inputs

Version 1.39.2:
- further fix to cope with the upcoming change
  to C23 as default in R 4.5.0

Version 1.39.1:
- added USE_C17 to DESCRIPTION as SystemRequirements to cope with the upcoming change
  to C23 as default in R 4.5.0

Version 1.37.4:
- change of interface of msaPrettyPrint() function in order to allow for a
  workaround for texi2dvi() problems (using quiet=TRUE and index=FALSE together
  throws an error)

Version 1.37.3:
- fix of major bug in the Muscle interface

Version 1.37.2:
- further fix of ClustalOmega makefile and source code to ensure compatibility
  with new Rcpp version (further adaptations for MacOS platform)

Version 1.37.1:
- fix of ClustalOmega makefile and source code to ensure compatibility with
  new Rcpp version

Version 1.35.5:
- major update of package help page man/msa-package.Rd

Version 1.35.4:
- fixes to account for move of substitution matrices from 'Biostrings' to 'pwalign'
  package

Version 1.35.3:
- changed e-mail address of maintainer
- updated README.md and formatting of package vignette
- updated references in documentation

Version 1.35.2:
- update of msaMakevars.win in ClustalW to avoid problems arising from compiling
  ClustalW with C++ 17: added -std=c++14

Version 1.35.1:
- update of some Makevars and Makefiles to avoid compliation issues on FreeBSD
  + minor adaptation in vignette
- minor fix in src/ClustalOmega/src/RClustalOmega.cpp (bug in Rprintf arg list)

Version 1.33.2:
- update of Makevars: added -lpthread to PKG_LIBS in order to make sure that
  package also builds correctly on Bioconda

Version 1.33.1:
- update of msaConsensusSequence() and msaConsensusSequence() methods to
  account for recent change in function Biostrings::consensusMatrix()

Version 1.31.7:
- changes of Version 1.31.6 undone (fix did not work on Mac OS)
- update of ClustalW makefile to avoid problems arising from compiling
  ClustalW with C++ 17: added -std=c++14

Version 1.31.6:
- update of ClustalW makefile to avoid problems arising from compiling
  ClustalW with C++ 17: added -D_HAS_AUTO_PTR_ETC=1

Version 1.31.5:
- update of Muscle source code to avoid problems arising from compiling
  Muscle with C++ 17: renamed type 'byte' to 'MByte'

Version 1.31.4:
- updated src/Muscle/subfams.cpp to avoid conflicting definitions of
  INFINITY on some Mac systems

Version 1.31.3:
- updated config.sub and config.guess in source code of ClustalW and
  ClustalOmega to solve compilation issues on aarch64 (thanks to Yikun Jiang
  for contributing this fix!)

Version 1.31.2:
- msa() function changed such that it also works if the package
  is not attached to the workspace

Version 1.31.1:
- update of gc

Version 1.29.3:
- fix for possibly malformed inputs: all sequences are forced to
  uppercase characters (previously, ClustalW and ClustalOmega produced
  wrong results when called with lowercase sequences)

Version 1.29.2:
- fix in texshade.sty as suggested on TeXshade homepage at CTAN

Version 1.29.1:
- fix in argtable library (ClustalOmega) to avoid compilation errors on
  newest Mac OS

Version 1.27.2:
- applied patch to allow msa to work with the new Windows UCRT toolchain

Version 1.27.1:
- workaround for problems running texi2dvi() on R 4.2.0; those occurred 
  during package checks when running some examples and the vignette code
- updated URLs and DOIs (now requires R version >= 3.3.0)
- fixed msaConvert() function to now work well with newer versions of the
  'ape' package (now requires at least version 5.2)

Version 1.25.3:
- further changes to get rid of compiler warnings

Version 1.25.2:
- removed build/ directory from repo to avoid installation problems

Version 1.25.1:
- update of gc
- minor changes to get rid of compiler warnings

Version 1.23.1:
- updated texshade.sty to newest version

Version 1.21.1:
- changed msaClustalW() examples to run smoothly on Windows with R 4.0.x
- added warning to msaClustalW() help page regarding cluster="upgma" on
  Windows

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
- fixed src/Makevars.win

Version 1.11.1:
- minor fix in ClustalW

Version 1.11.2:
- fix of code for using custom substitution matrices in ClustalW

Version 1.7.2:
- fix for new clang 4 compiler on Mac OS

Version 1.7.1:
- additional conversions implemented for msaConvert() function
- added a new method msaConsensusSequence() that extends the
  functionality provided by Biostring's consensusString() method
- added a new method msaConservationScore()
- print() method extended such that it now also allows for
  customization of the consensus sequence (via the new
  msaConsensusSequence() method)
- package now depends on Biostrings version >= 2.40.0 in order
  to make sure that consensusMatrix() also works correctly
  for masked alignments
- corresponding changes in documentation and vignette

Version 1.5.5:
- fixes in ClustalOmega source code to ensure Windows compatibility of
  GCC6 compatibility fix

Version 1.5.4:
- bug fix in msaClustalW(): unsupported parameter 'tree' deactivated
- fixes in ClustalOmega source code to ensure GCC6 compatibility
- fix in msaConvert() function to improve safety of call to suggested
  package 'phangorn'

Version 1.5.3:
- additional conversions implemented for msaConvert() function
- corresponding changes in documentation

Versions 1.5.1 / 1.5.2:
- version number bumps for technical reasons related to Bioconductor
  build servers

Version 1.3.7:
- fixes in msaPrettyPrint() function

Version 1.3.6:
- msaPrettyPrint() now also accepts dashes in file names
- added section about pretty-printing wide alignments to package
  vignette

Version 1.3.5:
- adaptation of displaying help text by msa() function 

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 1.1.3: 
- 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 1.0.0:
- first official release as part of Bioconductor 3.1
