Ned,
>1
aaaaaaaaa
>2
ttttttttt
>3
aaaaaaatt
>4
tttttttaa
>5
ataaatatt
In the above example, we should see 1&3 group together, & 2&4 due to shared similarities. Omit sequence 5 & try it.
With sequence 5 added, you may note that it is overall more similar
at any given loci to 1&3 as comparted to 2&4, & so should appear as a sister group to 1&3 rather than 2&4.
Hope that helps.
Mark
There are 10 kinds of people in this world; those that understand binary, & those that don't