Changes in version 1.43.1 o fix of bug that deleted sequence names if the sequences were read from FASTA file (all three alignment algorithms) Changes in version 1.41.3 o fix in ClustalOmega to better determine whether OpenMP is available o updated DESCRIPTION file to new format (Authors@R) Changes in version 1.41.2 o fix of memory leaks in Muscle (thanks for GitHub user Rong-Zh) Changes in version 1.41.1 o fix of compilation issues caused by ClustalOmega on arm64 systems Changes in version 1.39.5 o workaround to avoid segfault caused by ClustalOmega Changes in version 1.39.4 o fix of gc 8.2.8 source for Windows platform Changes in version 1.39.3 o upgraded gc library to version 8.2.8 o changed compiler standard to gnu++11 for ClustalOmega compilation on Linux/Mac o fixed a bug regarding passing file names as inputs Changes in version 1.39.2 o further fix to cope with the upcoming change to C23 as default in R 4.5.0 Changes in version 1.39.1 o added USE_C17 to DESCRIPTION as SystemRequirements to cope with the upcoming change to C23 as default in R 4.5.0 Changes in version 1.37.4 o 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) Changes in version 1.37.3 o fix of major bug in the Muscle interface Changes in version 1.37.2 o further fix of ClustalOmega makefile and source code to ensure compatibility with new Rcpp version (further adaptations for MacOS platform) Changes in version 1.37.1 o fix of ClustalOmega makefile and source code to ensure compatibility with new Rcpp version Changes in version 1.35.5 o major update of package help page man/msa-package.Rd Changes in version 1.35.4 o fixes to account for move of substitution matrices from 'Biostrings' to 'pwalign' package Changes in version 1.35.3 o changed e-mail address of maintainer o updated README.md and formatting of package vignette o updated references in documentation Changes in version 1.35.2 o update of msaMakevars.win in ClustalW to avoid problems arising from compiling ClustalW with C++ 17: added -std=c++14 Changes in version 1.35.1 o update of some Makevars and Makefiles to avoid compliation issues on FreeBSD + minor adaptation in vignette o minor fix in src/ClustalOmega/src/RClustalOmega.cpp (bug in Rprintf arg list) Changes in version 1.33.2 o update of Makevars: added -lpthread to PKG_LIBS in order to make sure that package also builds correctly on Bioconda Changes in version 1.33.1 o update of msaConsensusSequence() and msaConsensusSequence() methods to account for recent change in function Biostrings::consensusMatrix() Changes in version 1.31.7 o changes of Version 1.31.6 undone (fix did not work on Mac OS) o update of ClustalW makefile to avoid problems arising from compiling ClustalW with C++ 17: added -std=c++14 Changes in version 1.31.6 o update of ClustalW makefile to avoid problems arising from compiling ClustalW with C++ 17: added -D_HAS_AUTO_PTR_ETC=1 Changes in version 1.31.5 o update of Muscle source code to avoid problems arising from compiling Muscle with C++ 17: renamed type 'byte' to 'MByte' Changes in version 1.31.4 o updated src/Muscle/subfams.cpp to avoid conflicting definitions of INFINITY on some Mac systems Changes in version 1.31.3 o 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!) Changes in version 1.31.2 o msa() function changed such that it also works if the package is not attached to the workspace Changes in version 1.31.1 o update of gc Changes in version 1.29.3 o fix for possibly malformed inputs: all sequences are forced to uppercase characters (previously, ClustalW and ClustalOmega produced wrong results when called with lowercase sequences) Changes in version 1.29.2 o fix in texshade.sty as suggested on TeXshade homepage at CTAN Changes in version 1.29.1 o fix in argtable library (ClustalOmega) to avoid compilation errors on newest Mac OS Changes in version 1.27.2 o applied patch to allow msa to work with the new Windows UCRT toolchain Changes in version 1.27.1 o workaround for problems running texi2dvi() on R 4.2.0; those occurred during package checks when running some examples and the vignette code o updated URLs and DOIs (now requires R version >= 3.3.0) o fixed msaConvert() function to now work well with newer versions of the 'ape' package (now requires at least version 5.2) Changes in version 1.25.3 o further changes to get rid of compiler warnings Changes in version 1.25.2 o removed build/ directory from repo to avoid installation problems Changes in version 1.25.1 o update of gc o minor changes to get rid of compiler warnings Changes in version 1.23.1 o updated texshade.sty to newest version Changes in version 1.21.1 o changed msaClustalW() examples to run smoothly on Windows with R 4.0.x o added warning to msaClustalW() help page regarding cluster="upgma" on Windows Changes in version 1.17.2 o removed change history from package vignette for easier maintenance Changes in version 1.17.1 o fixed regular expression to comply with PCRE2 o fixed Windows makefile for gc lib o fixed Windows cleanup script o fixed src/Makevars.win Changes in version 1.11.2 o fix of code for using custom substitution matrices in ClustalW Changes in version 1.11.1 o minor fix in ClustalW Changes in version 1.7.2 o fix for new clang 4 compiler on Mac OS Changes in version 1.7.1 o additional conversions implemented for msaConvert() function o added a new method msaConsensusSequence() that extends the functionality provided by Biostring's consensusString() method o added a new method msaConservationScore() o print() method extended such that it now also allows for customization of the consensus sequence (via the new msaConsensusSequence() method) o package now depends on Biostrings version >= 2.40.0 in order to make sure that consensusMatrix() also works correctly for masked alignments o corresponding changes in documentation and vignette Changes in version 1.5.5 o fixes in ClustalOmega source code to ensure Windows compatibility of GCC6 compatibility fix Changes in version 1.5.4 o bug fix in msaClustalW(): unsupported parameter 'tree' deactivated o fixes in ClustalOmega source code to ensure GCC6 compatibility o fix in msaConvert() function to improve safety of call to suggested package 'phangorn' Changes in version 1.5.3 o additional conversions implemented for msaConvert() function o corresponding changes in documentation Changes in version 1.5.1 o version number bumps for technical reasons related to Bioconductor build servers Changes in version 1.3.7 o fixes in msaPrettyPrint() function Changes in version 1.3.6 o msaPrettyPrint() now also accepts dashes in file names o added section about pretty-printing wide alignments to package vignette Changes in version 1.3.5 o adaptation of displaying help text by msa() function Changes in version 1.3.4 o added function for checking and fixing sequence names for possibly problematic characters that could lead to LaTeX errors when using msaPrettyPrint() o corresponding changes in documentation o minor namespace fix Changes in version 1.3.3 o added function for converting multiple sequence alignments for use with other sequence alignment packages o corresponding changes in documentation Changes in version 1.3.2 o further fixes in Makefiles and Makevars files to account for changes in build system o update of citation information Changes in version 1.3.1 o fixes in Makefiles and Makevars files to account for changes in build system Changes in version 1.1.3 o bug fix related to custom substitution matrices in the MUSCLE interface o correction and updates of documentation Changes in version 1.1.2 o new print() function for multiple alignments that also allows for displaying alignments in their entirety (plus additional customizations) o 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. o strongly improved handling of custom substitution matrices by msaMuscle() o fix of improperly aligned sequence logos produced by msaPrettyPrint() o updated citation information Changes in version 1.1.1 o fix of msa() function Changes in version 1.0.0 o first official release as part of Bioconductor 3.1