v2.1 [Nov 20, 2010]
- 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"
