NEWS

---

msa 1.43.1

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

msa 1.41.3

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

msa 1.41.2

• fix of memory leaks in Muscle (thanks for GitHub user Rong-Zh)

msa 1.41.1

• fix of compilation issues caused by ClustalOmega on arm64 systems

msa 1.39.5

• workaround to avoid segfault caused by ClustalOmega

msa 1.39.4

• fix of gc 8.2.8 source for Windows platform

msa 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

msa 1.39.2

• further fix to cope with the upcoming change to C23 as default in R 4.5.0

msa 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

msa 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)

msa 1.37.3

• fix of major bug in the Muscle interface

msa 1.37.2

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

msa 1.37.1

• fix of ClustalOmega makefile and source code to ensure compatibility with new Rcpp version

msa 1.35.5

• major update of package help page man/msa-package.Rd

msa 1.35.4

• fixes to account for move of substitution matrices from 'Biostrings' to 'pwalign' package

msa 1.35.3

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

msa 1.35.2

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

msa 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)

msa 1.33.2

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

msa 1.33.1

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

msa 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

msa 1.31.6

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

msa 1.31.5

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

msa 1.31.4

• updated src/Muscle/subfams.cpp to avoid conflicting definitions of INFINITY on some Mac systems

msa 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!)

msa 1.31.2

• msa() function changed such that it also works if the package is not attached to the workspace

msa 1.31.1

• update of gc

msa 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)

msa 1.29.2

• fix in texshade.sty as suggested on TeXshade homepage at CTAN

msa 1.29.1

• fix in argtable library (ClustalOmega) to avoid compilation errors on newest Mac OS

msa 1.27.2

• applied patch to allow msa to work with the new Windows UCRT toolchain

msa 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)

msa 1.25.3

• further changes to get rid of compiler warnings

msa 1.25.2

• removed build/ directory from repo to avoid installation problems

msa 1.25.1

• update of gc
• minor changes to get rid of compiler warnings

msa 1.23.1

• updated texshade.sty to newest version

msa 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

msa 1.17.2

• removed change history from package vignette for easier maintenance

msa 1.17.1

• fixed regular expression to comply with PCRE2
• fixed Windows makefile for gc lib
• fixed Windows cleanup script
• fixed src/Makevars.win

msa 1.11.2

• fix of code for using custom substitution matrices in ClustalW

msa 1.11.1

• minor fix in ClustalW

msa 1.7.2

• fix for new clang 4 compiler on Mac OS

msa 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

msa 1.5.5

• fixes in ClustalOmega source code to ensure Windows compatibility of GCC6 compatibility fix

msa 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'

msa 1.5.3

• additional conversions implemented for msaConvert() function
• corresponding changes in documentation

msa 1.5.1

• version number bumps for technical reasons related to Bioconductor build servers

msa 1.3.7

• fixes in msaPrettyPrint() function

msa 1.3.6

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

msa 1.3.5

• adaptation of displaying help text by msa() function

msa 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

msa 1.3.3

• added function for converting multiple sequence alignments for use with other sequence alignment packages
• corresponding changes in documentation

msa 1.3.2

• further fixes in Makefiles and Makevars files to account for changes in build system
• update of citation information

msa 1.3.1

• fixes in Makefiles and Makevars files to account for changes in build system

msa 1.1.3

• bug fix related to custom substitution matrices in the MUSCLE interface
• correction and updates of documentation

msa 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

msa 1.1.1

• fix of msa() function

msa 1.0.0

• first official release as part of Bioconductor 3.1