|FROM ||Ruben Safir
|SUBJECT ||Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
|From learn-bounces-at-nylxs.com Thu Jan 26 18:50:13 2017
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From: Ruben Safir
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Date: Thu, 26 Jan 2017 18:49:50 -0500 (EST)
Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
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-- forwarded message --
From: ruben safir
Subject: Re: Felsenstein Phylogenies
Date: Thu, 26 Jan 2017 06:49:02 -0500
Organization: PANIX Public Access Internet and UNIX, NYC
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On 01/26/2017 06:46 AM, ruben safir wrote:
> On 01/25/2017 09:35 PM, John Harshman wrote:
>> On 1/25/17 3:53 PM, Ruben Safir wrote:
>>> Does anyone have the above text handy? I think what he wrote with
>>> regard to Subtree Programming and Grafting is incorrect.
>>> If you have 2 subtrees n1 and n2,the number of neighbors should be (2n1
>>> -4) * (2n2 - 4) --- not addition
>>> each spot has 2n-3 - 1 permutations.
>>> He doesn't explain what external branches are either.
>> The book you're referring to is called Inferring Phylogenies and the
>> procedure you're talking about is called subtree *pruning* and
>> *regrafting*. The number of rearrangements given a particular subtree
>> should be equal to the number of branches on the second subtree, which
>> is twice the number of taxa minus 3.
>> I don't currently have a copy handy. Please explain more clearly what
>> Felsenstein says about it and what you think it should say.
> Correct, what it does say is that once you divide the tree there would
> be 2n1 - 3 - 1 reassertion points for the tree. Then after that he is
> not clear to me. He says
> "In fact considering both subtrees (no having n1 species and the one
> having n2 species, there are
> (2n1-3-1) + (2n2-3-1 ) = (2n-3-1) = 2n-8
> neighbors generated at each interior branch."
> This assumes n1 + n2 = n.
> I guess that is all the possible combinations assuming the same
> attachment locations for the trees, examining one tree at a time.
> Then he states that external nodes (which is not defined) is 2n-6.
> Without proof I'll accept that for a moment (and I think it corresponds
> to binary tree theory), but I'm not sure that an exterior node is. That
> is a node that connects to leafs?
> Finally, the last unclear sentence, at least to me, states:
> "Thus, as there are n exterior branches on an unrooted bifurcating tree
> and n-3 interior branches, the total number of neighbors examined by SPR
> will be
> That is where he lost me. Then he follows up
> and he says tha there are 288 neighbors for n=11
> "Of course, 2(n-3)=16 of them are the same as NNI"
> For TBR he says that there is no general formula for the number of
> neighbors that will be examine. That made be stand on the edge of my
> seat? Say what? Then what are we doing?
I have an electronic version of the text you can borrow but I don't want
to post it here.
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