Inferring Phylogenies by Joseph Felsenstein

By Joseph Felsenstein

Felsenstein's ebook is superb as a reference while taking a look up the key options and checks for phylogeny.

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For 50 ~ ecies, one is approaching Eddington's famous number, the number of electrons Jl the visible universe. The counting of trees has been a mathematician's recreation since the pioneer, g work of Cayley (1857, 1889). 1. He used generating function methods, as did Cayley. The ~inlple argument used here is due to Cavalli-Sforza and Edwards (1967). Moon 1970) has reviewed many other counting problems involving labeled trees. But ,_ artially-labeled cases like those we consider have largely been left to biologists to cmmt.

Nearest-neighbor interchanges Nearest-neighbor interchanges (NNI) in effect swap two adjacent branches on the tree. A more careful description is that they erase an interior branch on the tree, and the two branches connected to it at each end (so that a total of five branches are erased). This leaves four subtrees disconnected from each other. 2: The process of nearest-neighbor interchange. An interior branch is dissolved and the four subtrees connected to it are isolated. These then can be reconnected in two other ways.

When n = 4, there are 15 tree topologies but 18 labeled histories, a small increase. But when n = 10, the 34,459,425 tree topologies lead to 2,571,912,000 labeled histories, an increase by a factor of almost 75. Perspective Knowing exactly how many tree topologies or tree shapes there are in various cases is not particularly important, unless one is enumerating them in a computer program and wants to know whether the program has found each of them exactly once. The point is that there are very large numbers of them, and these numbers rise exponentially.

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