COMP571 (Fall 2020, a.k.a. COVID times)
Important note: The information contained in the course syllabus, other than the absence policies, may be subject to change with reasonable advance notice, a...
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Calculating the likelihood for an ultrametric tree (example)
In this example we will calculate the likelihood \(P(D|T,h)\) where \(D\) is a single site, \(T\) is a rooted tree topology, and \(h\) is the node heights fo...
Hill climbing and NNI
The Sankoff algorithm can efficiently calculate the parsimony score of a tree topology. Felsenstein’s pruning algorithm can efficiently calculate the probabi...
Long branch attraction (in the Felsenstein zone)
Long branch attraction is the phenomenon where two branches which are in truth not sisters are inferred to be sister branches when using maximum parsimony in...
Likelihood of a tree
The likelihood of a tree is the probability of a multiple sequence alignment or matrix of trait states (commonly known as a character matrix) given a tree to...