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Alright. Monday we have a test, and now I was making a practise test.

We have to make a maximum parsimony tree. We must do that monday again, so I want to know if I am thinking wrong, or if the answer model is incorrect.

The sequences are:

Seq     1    2    3    4    5    6    7   
1       A    T    A    A    G    C    C
2       T    C    A    C    C    T    G
3       A    T    C    C    G    A    C
4       T    G    C    A    C    T    G

This results in:

          1    2    3    4
----------------------------
   1  |   
   2  |   6
   3  |   3    6
   4  |   6    3    6

And eventually, this results in:

          1,3     2,4
-----------------------------
1,3  |
2,4  |    6

This is the tree in the correction model:

enter image description here

My tree has two 1,5's instead of the two 3's at the root of the tree. Because 6 is the last distance. 6/2 = 3, so both branches should get a distance of 3. But, according to some examples I saw on the internet, it's a distance of 3 to the end of tree then, and not 3 to the next node. And there is already a distance of 1,5 in further benches at both sides, so only 1,5 remains (because 3 - 1.5 = 1.5).

So, am I wrong, or is the correction model wrong? Then I know how I must do it at the real test.

Sorry if my English is bad, and it's a little hard to explain because English is not my native language, but if I am right, you should know what I mean.

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    $\begingroup$ From your description, this is a distance-based clustering tree (UPGMA), not a parsimony tree. And in this case I believe you are correct, since if you sum up all branches from 1 to 2 or 3 to 4 (1.5 x 4) you will have the original pairwise distances. (The same for 1-3, and 2-4, which are easier.) $\endgroup$ – Leo Martins Jun 17 '17 at 23:08

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