What's new in ClustalX 2.1
Jul 2, 2012
- Fixed bug 196 "clustalx: user feedback about use of secondary structure printed to console" - secondary structure is now used if specified in Alignment -> Alignment Parameters -> Secondary Structure Parameters UserParameters->getGui() should be used when ClustalW code needs to know if a function has been called from ClustalX
- Fixed bug 204 "Nexus alignment format contain invalid line" - the amino acid alphabet line has been removed
- Missing/corrupted file names in ClustalX status messages have been fixed
- Fixed bug 175 "msf/pileup files cannot be read if sequences names are all numbers" - this happened if a line such as 528244 .......... .......... .......... .......... .......... was present in the first block of the file
- Fixed bug 192 "Alignment in Phylip Format broken for big Alignments"
- Fixed bug 198 "Warning about divergent sequences gets printed to console in ClustalX"
- Fixed bug 151 "clustalx doesn't switch to profile alignment mode when profile12 is given on cmdline"
New in ClustalX 2.0.12 (Jan 4, 2010)
- Fixed bug 189 "Fixed filename used for iteration": Now Creating temporary file and added error check
- Fixed bug 180 "Pairwise NJ tree: final bracket missing"
- Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with high identity": Using relative error now to avoid unsafe comparison which led to incorrect branching
- Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well"
- Fixed bug 162 "percent identity file option in clustalW not working": Added -pim as command line option. See help
- Fixed bug 155 "upgma trees cannot be read"
- Fixed bug 147 "report duplicate sequences": "ClustalW/X now report offending sequences which are empty, duplicates etc
- Fixed bug 134 "Exit when encountering unrecognized cmdline params": ClustalW now exits when encountering invalid values for command line arguments instead of just reverting to default values
- Fixed bug 185 "clustal alignments differ between interactive and commandline mode" window-gap and ktuple initialisation now fixed and made the same between commandline and interactive mode
- Fixed bug 184 "error messages are send to stdout"
- Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA code (see RootedGuideTree.cpp)
- General code cleanup:
- Introduced return values where control reached end of non-void function
- Removed unused variables
- Removed comparison between signed and unsigned integer expressions
- Removed deprecated conversion from string constant to char.
New in ClustalX 2.0.11 (Jan 4, 2010)
- Fixed file extension bug 166 in interactive mode.
- Fixed bug 169, memory violation for DNA/RNA k-tuple.
- Cut down distance calculation, symmetric matrix.
New in ClustalX 2.0.10 (Oct 17, 2008)
- Fixed g++-4.3 compilation errors
- Added new -quiet command line flag
- Added new -stats= command line flag
- Fixed bug 142: command separator can now be mixed "/" and "-" on all platforms
- Fixed bug 141: profile merging and saving failed
- Fixed bug 139: saving of column quality scores
- Updated help files (new flags, new colour parameter format)
New in ClustalX 2.0.8 (Jun 10, 2008)
- Implemented maxseqlen cmdline switch
- Updated help-file
- Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac)
- Fixed bug 133: providing profiles on command line fails (ClustalX)
- Fixed bug 125: Angle bracket inside sequence
- Fixed bug 129: Early exit on empty sequence
- Fixed a couple of possible memory leaks