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DATE 2017-01-01

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MESSAGE
DATE 2017-01-26
FROM Ruben Safir
SUBJECT Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
From learn-bounces-at-nylxs.com Thu Jan 26 18:50:06 2017
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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 --
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NNTP-Posting-Date: Thu, 26 Jan 2017 10:48:51 -0600
Subject: Re: Felsenstein Phylogenies
Newsgroups: sci.bio.paleontology
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<429a9d55-1da8-b068-0049-4029944f897c-at-mrbrklyn.com>

From: John Harshman
Date: Thu, 26 Jan 2017 08:48:51 -0800
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Xref: panix sci.bio.paleontology:67127

On 1/26/17 3:49 AM, ruben safir wrote:
> 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
>>
>> n(2n-6)+(n+3)(2n-8)"
>>
>> That is where he lost me. Then he follows up
>> and he says tha there are 288 neighbors for n=11
>> and
>> "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.
>
Just copy and paste the relevant parts. That way you avoid confusing typos.
-- end of forwarded message --
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