Nested Hierarchy and Bootstrap Values

@AndyWalsh There are some strangely dressed people here who would like a word with you …

:wink:

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Oh, yeah I am. Sorry, I thought you were saying there was something specific about this thread that related to r/debateevolution. :sweat_smile:

I used to be a creationist there too, and in fact I wouldn’t have escaped creationism without your help.

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Should be pretty good: not as fast as RAxML but. somewhat faster than PAUP*. All of them work well.

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IQ-TREE is another excellent option for maximum likelihood phylogenetic inference. I use it pretty regularly.

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Oh by the way, just a (to me) funny coincidence I noticed a few years ago when I first started looking into how phylogenetic algorithms actually work.
I realized the algorithms are actually similar to evolutionary algorithms, that climb hills in a sort of “tree space” that is searched for the “most fit” tree according to whatever criterion the algorithm is based on(minimum evolution, shortest total branch length, conditional probability of the data, or whatever), and there is something analogous to both selection and mutation going on with branch swapping, rearrangement and stuff like that and then comparing the fitness of trees.

Just thought it was funny how evolution is in effect employed to find out how something else evolved.

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I dunno, they seem normally dressed to me…

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Sounds more like a creationist’s test result.

Thee are legion! :slight_smile:

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Yes, and evolutionary algorithms have been used to search for maximum likelihood trees. (It is important to let the users know that just because one is trying to reconstruct evolution, the best method need not be using “evolution”).

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Even better, look at GARLI. It uses an explicitly evolutionary process, a genetic algorithm, for tree selection.

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