Annotate pairwise alignment with query sequence quality scores

Question

[Thomas]

Hello,

I have a pairwise alignment of a reference sequence and a query sequence. The query sequence has been inferred from Sanger sequencing, and has a series of Phred quality scores associated with it.

Once an alignment has been generated, I would like to annotate the alignment using the quality scores of the query sequence. Preferably, this would be in the form of colour-coding the query sequence according to quality score.

Is there a tool that would allow me to do this relatively quickly and easily?

Thanks!