further fix of ClustalOmega makefile and source code to ensure compatibility
with new Rcpp version (further adaptations for MacOS platform)
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 1.35.0
new branch for Bioconductor 3.19 devel
msa 1.34.0
release as part of Bioconductor 3.18
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 1.33.0
new branch for Bioconductor 3.18 devel
msa 1.32.0
release as part of Bioconductor 3.17
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 1.31.0
new branch for Bioconductor 3.17 devel
msa 1.30.0
release as part of Bioconductor 3.16
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 1.29.0
new branch for Bioconductor 3.16 devel
msa 1.28.0
release as part of Bioconductor 3.15
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 1.27.0
new branch for Bioconductor 3.15 devel
msa 1.26.0
release as part of Bioconductor 3.14
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 1.25.0
new branch for Bioconductor 3.14 devel
msa 1.24.0
release as part of Bioconductor 3.13
msa 1.23.1
updated texshade.sty to newest version
msa 1.23.0
new branch for Bioconductor 3.13 devel
msa 1.22.0
release as part of Bioconductor 3.12
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 1.21.0
new branch for Bioconductor 3.12 devel
msa 1.20.0
release as part of Bioconductor 3.11
msa 1.19.0
new branch for Bioconductor 3.11 devel
msa 1.18.0
release as part of Bioconductor 3.10
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 1.17.0
new branch for Bioconductor 3.10 devel
msa 1.16.0
release as part of Bioconductor 3.9
msa 1.15.0
new branch for Bioconductor 3.9 devel
msa 1.14.0
release as part of Bioconductor 3.8
msa 1.13.0
new branch for Bioconductor 3.8 devel
msa 1.12.0
release as part of Bioconductor 3.7
msa 1.11.2
fix of code for using custom substitution matrices in ClustalW
msa 1.11.1
minor fix in ClustalW
msa 1.11.0
new branch for Bioconductor 3.7 devel
msa 1.10.0
release as part of Bioconductor 3.6
msa 1.9.0
new branch for Bioconductor 3.6 devel
msa 1.8.0
release as part of Bioconductor 3.5
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 1.7.0
new branch for Bioconductor 3.5 devel
msa 1.6.0
release as part of Bioconductor 3.4
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 1.5.0
new branch for Bioconductor 3.4 devel
msa 1.4.0
release as part of Bioconductor 3.3
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 1.3.0
new branch for Bioconductor 3.3 devel
msa 1.2.0
release as part of Bioconductor 3.2
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 1.1.0
new branch for Bioconductor 3.2 devel
msa 1.0.0
first official release as part of Bioconductor 3.1