> Your implied question seems to be "How do I know whether my MSA is > good?" Errors in MSAs arise from two factors. ...
The correct multiple alignment would be the actual reconstruction of the evolutionary relationship of the sequences concerned. This may not be the optimal alignment of the present-day sequences, and it isn't knowable from them, especially if the history is long. The best that any alignment program could do in principle is to calculate the different possible alignments, with likelihoods. But that is a too complicated result to work with - so one tends to settle for a single multiple alignment, with an unknown relationship to the optimal alignment, and an unknown relationship to the true history. ____________________________________________ Chris Morris chris.mor...@stfc.ac.uk Tel: +44 (0)1925 603689 Fax: +44 (0)1925 603634 Mobile: 07921-717915 Skype: chrishgmorris http://pims.structuralbiology.eu/ http://www.citeulike.org/blog/chrishmorris Daresbury Lab, Daresbury, Warrington, UK, WA4 4AD
