On Fri, Nov 19, 2010 at 5:16 AM, Dr G. Bunkoczi
Would it be sufficient to provide an option, so that one can specify the index of the target sequence in the alignment file?
in the interest of automation, i guess - though the titles (the stuff on the line starting with ">") can get pretty disgusting if you keep everything from the database it came from : non-alphabetic characters, spaces,
Would it be better to provide the target sequence, and let Sculptor figure out the index itself?
can't say if its better, but if it works - why not. i have seen programs where you say e.g. "fubar" and then the alignment has a part with ">fubar" then everything between ">fubar" and the next ">" is defined as the target sequence (IIUC). ... anyways, how is the target sequence used that a consensus sequence couldn't be used instead? i mean, the model looks like it has one applied to it. -Bryan