Charlie Bond's ALINE program (http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/) can handle upper/lower case sequences.
In the menu bar: Tools > Alignment > Align All Sequences does the job (using clustalw as a back-end IIRC) without changing cases. Best, Stephen 2009/9/16 MARTYN SYMMONS <[email protected]>: > Dear All > - I am looking for a multiple alignment program that will work > with upper and lower case letters in the sequences and preserve them through > to the output. I used to use PILEUP but that is no longer supported here. > Any suggestions much appreciated. > regards > Martyn > > Martyn F. Symmons > Department of Pathology > University of Cambridge > ---------------------------- > 'Gun fhaillin 'san fhairge..' > (said of Griomasaigh boats) > -- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
