Felsenstein's tree-pruning algorithm: Difference between revisions

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== Details ==

[[File:Tree_exemple.png|thumb|A simple phylogenetic tree exempleexample made from arbitrary data D]]

The '''likelihood''' of a tree <math>T</math> is, by definition, the probability of observing certain data <math>D</math> (<math>D</math> being a nucleotide sequence alignment for example ''i.e.'' a succession of <math> n </math> DNA site <math> s </math>) given the tree. It is often written : <math>P(D|T)</math>.

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</math>

If I reuse the exempleexample above, <math>D_1</math> tree would be:

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<math> w_k (X) = ( \sum_Y p_{X \rightarrow Y} \centerdot w_i (Y)) \centerdot ( \sum_Z p_{X \rightarrow Z} \centerdot w_j (Z)) </math>

where <math> Y </math> and <math> Z </math> are also DNA bases. <math> p_{ X\rightarrow Y} </math> is the transition probability from nucleotide <math>X</math> to nucleotide <math> Y </math> (idem for <math> p_{X \rightarrow Z} </math>). <math> w_i(Y) </math> is the partial likelihood of the daughter node <math>

i

</math>, evaluated on nucleotide <math> Y </math> (idem for <math>

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== Algorithm ==

== Simple ExempleExample ==

==References==