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Can homoplasy be measured?

marjon van dijk m.vandijk at bioch.kun.nl
Sat Jan 9 14:22:37 EST 1999

Given a multiple alignment of ten mammal sequences, is it possible to judge
objectively that two mammals with the same amino acid on one site and the
other eight mammals having another amino acid on this site have a shared
derived character or that it is homoplasy? So, are there methods to
calculate the rate of homoplasy for each site in the alignment?

In order to compare different genes is it, knowing that not all sites
change equally, possible to calculate the rate of homoplasy for a complete

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