How To Interpret Multiple Alignment Score In Clustalw?

Question

[Muzna]

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?

Answer 1

[Rm]

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)

[Bilouweb]

I agree with this answer. The sum-of-pairs score is well explain page 304 of the paper.

[Mirko]

The requested URL /~dehne/publications/2-68.pdf was not found on this server.

Do you happen to have an alternative link?