WongPeiFong
commented
4 days ago Hello, Got it. Sorry for the late reply. For the HW2 i forget how root the tree in MEGA, so the tree is not correctly constructed.. By the way i have uploaded my HW3 in Github. Choosing only one organism and find 10 of them species with 2 genes sequences available in database was quite difficult so i decided to compare between 10 different Model organisms instead
Wong Pei Fong
Mikhail Raiko @.***> 於 2024年10月31日 週四 上午1:16寫道：
Thanks, good work. But I have few concerns. Both trees in your work seem rooted incorrectly - at some arbitrary point, instead of outgroup. We can use Pan (chimpanse) samples to obtain correct branching order for all other species, and Neanderthal or Denisova - to root the tree of the human populations. Also, I didn't get your calculation. The whole idea of this work was to obtain the number of mutations from your data, comparing samples from both clades after the first split (to get it correctly, we need to root our tree properly - see above). And then we can directly compare them. And in your case you got thes 75-150 mutations out of blue - it diminishes the whole sense of this homework. Anyway, it's a honest work, just pay attention to your results, and ask if there is something unclear.
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Thanks, good work. But I have few concerns. Both trees in your work seem rooted incorrectly - at some arbitrary point, instead of outgroup. We can use Pan (chimpanse) samples to obtain correct branching order for all other species, and Neanderthal or Denisova - to root the tree of the human populations. Also, I didn't get your calculation. The whole idea of this work was to obtain the number of mutations from your data, comparing samples from both clades after the first split (to get it correctly, we need to root our tree properly - see above). And then we can directly compare them. And in your case you got thes 75-150 mutations out of blue - it diminishes the whole sense of this homework. Anyway, it's a honest work, just pay attention to your results, and ask if there is something unclear.