MBIO 3430 Lecture Notes - Lecture 16: Upgma, Neighbor Joining, Distance Matrix
11 Nov 2018
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Argument: if there is a trend in a data set, resampling should not dilute the trend. O ea(cid:272)h (cid:271)ootstrap repli(cid:272)ate (cid:374)o(cid:449) has to (cid:271)e a(cid:374)alyzed a(cid:374)d all (cid:862)trees are (cid:272)o(cid:373)pared(cid:863) Usually to be significant 95% of bootstrap replicated should show the same trend in order to be significant (but lower numbers are also sometimes accepted) Maximum likelihood (ml) apply evolutionary models. Complex sequences added separately to the tree and for each site (change) and probability is generated to evaluate how likely such a mutation would have occurred (based on an evolutionary model at the ancestral node (~character state) Sum of all probabilities gives the overall probability for the tree. The tree with the ml highest probability is viewed as best possible tree. Very slow many trees are built during this process and evaluated based on the ml criterion get one ml tree.
