Acces the ClustalW multiple sequence alignment program and modify the content of a selected project in an integrated environment for performing the necessary alignments and analyzing the results by viewing them in a preview window and checking the signifying color markings.
Clustal X is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results.
The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment.
You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment.
Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted.
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"
