To Whom It May Concern, Sorry to bother you with what is likely a fairly simple problem, but I have trying to figure this out myself for several days and just can't figure out how to do it. I have a set of 8766 genes that I would like to test for positive selection in using various other programs (HyPhy for example). To do this I obviously need an alignment of these genes across various species, but I just can't figure out how to get the alignment in a fasta format. For example, I have a BED12 file from UCSC with the data for the 8766 genes, I thought the easiest way was to use the "Stitch Gene blocks" option and then select locally cached alignments as the MAF source for the species I care about. However, because these 8766 genes have multiple transcripts I end up with 23,581 regions. Is there a way to merge the multiple regions for each gene into a single region for the longest transcript? Then I should have 8766 regions and can use Stitch Gene blocks". (Unless there is a more economical way to do this.)\ Thanks Vinny Vincent J. Lynch, Associate Research Scientist Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute Yale University http://pantheon.yale.edu/~vjl4/profpage/ "There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." -C. Darwin, 1859 (Walker, Wisconsin, Madison, Maddow, Tea Party, Obama, global warming)