When we use CLUSTALW for multiple alignment of aa, then on result page first appear pairwise alignment score which is in percentages, then appear multiple alignment score. I am unable to understand that one multiple alignment score. Can anyone please explain it to me how to read it or interpret it?
follow these links: http://www.ebi.ac.uk/Tools/msa/clustalw2/help/faq.html#21
http://people.scs.carleton.ca/~dehne/publications/2-68.pdf (page 304-305)