Thank you Dan for the suggestion, I still did not get this. I have downloaded annotation file for one of my alignments but cannot understand how will i give the position/column to be highlighted for specific sequence. Please could you explain in little detail?

Check out the section in that link for associating an annotation track with a particular sequence. I don't know if you can automate highlighting a particular residue but you can make a seperate track that indicates a single column (perhaps with a bar graph format?) and have it linked to a particular sequence or group of sequences. Its not perfect but it may be as close as you can get in an automated fashion. You could make a histogram track for instance with a maximum score for only the column of interest and zero elsewhere, then link it to the sequence(s) of interest