I would like to do a pairwise/multiple sequence alignment for a gene from two/three species and then record in a separate file the exact positions of perfect identity between the sequences. Is there a tool that does this already? Or is there any option in blast/clustal that could help in recovering this information ?
Will be very thankful for your time and responses.
Have you tried GBlocks? http://molevol.cmima.csic.es/castresana/Gblocks.html I know it can extract highly conserved regions from an alignment, but not sure if you can configure it to extract only perfect matches. Edit: here is the webserver: http://www.vardb.org/vardb/analysis/gblocks.html