I want to do essentially a Clustal alignment or anything similar, but with a twist -- I have a situation where parts of my sequence may have become inverted. Reverse-complementing the whole thing is not an option. I would like it to call automatically whether there is a "decent" match in the forward, or reverse-complement, or neither direction, and then present that in some meaningful way. Do you know of a software will at least try to do such a thing for me?
If you can do a blast comparison between two (or more) sequences, ACT is a very simple program for visualization of that output file. Nucleotide sequences with 77%+ ID in the same orientation are colored red while blue shows where the two sequences are homologous but inverted. The entire comparison can than be exported as a png/jpeg.
Hi, you can use mafft with the --adjustdirection option (command line).
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