I am using standalone blast and I want to see alignment summary like the one produced in the online version on ncbi website. Basically, I want to see where all my HSPs are aligning in the entire query sequence. But the stand alone version of blastn only shows local alignments between HSPs and the part of query. Any ideas how can I see the subject sequences aligned to the whole query sequence, and not just local alignments? I want to visualize the globally how much and which parts of query are aligned.
Thanks a lot for help!