[Bioperl-l] tiling hits to multiple alignment

[Babenko, Vladimir (NIH/NLM/NCBI)]

    I wonder if there is any optimal way/template to arrange the blast hits
separately along the query in a form of multiple alignment?

I have no problems in pairwise AlignIO object creation from blast output,
thanks to SearchIO, but as for the whole hit set I have no clear idea.

   Could there be some “natural” way to do that?

        Thanks,

         Vladimir