|FROM ||Ruben Safir
|SUBJECT ||Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
|From learn-bounces-at-nylxs.com Thu Jan 26 18:50:19 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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NNTP-Posting-Date: Thu, 26 Jan 2017 10:56:45 -0600
Subject: Re: Felsenstein Phylogenies
From: John Harshman
Date: Thu, 26 Jan 2017 08:56:45 -0800
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Xref: panix sci.bio.paleontology:67128
On 1/26/17 3:46 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.
Which it must.
> I guess that is all the possible combinations assuming the same
> attachment locations for the trees, examining one tree at a time.
Not sure what you meant by that.
> 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?
I don't know what 2n-6 is, based on your description, but from the
formula below it appears to be the number of subtrees that could be
attached to any terminal branch of the tree, i.e. the number of subtrees
not containing that branch.
> 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.
Why? Did his formula have n+3 when it should have had n-3? Otherwise I
see no problem.
> 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"
Why is that a problem?
> 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 do not understand your problem there.
For all of these, you need to explain what you think the problem is.
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