Hi,

I'm a newcomer here so maybe my question is trivial:
 I'm working on a project focused on ultradeep sequencing analysis of an amplicon (2-3kb). Basically what I need to do is to align my sequences (from FLX and GAII) to a known amplicon and to detect and characterize the whole set of mutations (frequency and aa substitutions mostly).
I tried to perform this task with Galaxy, however the only alignment tool I found under the 'short read analysis' is the Megablast, which allows me to align only to nt or wgs but not to 'custom' references. I also tried the supermatcher under the EMBOSS section with quite poor results.
Is there any way to perform this kind of analysis by using Galaxy from the groud up or shall I need to refer to external alignment tools?

Regards,
Rocco

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