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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 18:49:55 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 --
Path: reader1.panix.com!panix!not-for-mail
From: Ruben Safir
Newsgroups: sci.bio.paleontology
Subject: Re: Felsenstein Phylogenies
Date: Thu, 26 Jan 2017 22:11:31 +0000 (UTC)
Organization: PANIX Public Access Internet and UNIX, NYC
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John Harshman wrote:
> 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.

what does that have to do with counting neighbors though.

>
>> 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.
>
> Why? Did his formula have n+3 when it should have had n-3? Otherwise I
> see no problem.
>

No, because the formular seems to have no basis in the problem. It
seems like random gibberish. I've consulted with a numer of
mathamaticians and Comp Sci people and so far nobody understands how
this is derived or the meaning of his terminaolgy. That is why I posted
here :(

>> 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"
>
> 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.
>

the sentence is devoid of specific meaning and is contra to what he just
solved.

> For all of these, you need to explain what you think the problem is.
>
>

His difinition of terms are not clear and the formulas don't represent
the problem being solved.
-- end of forwarded message --
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