|FROM ||Ruben Safir
|SUBJECT ||Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
|From learn-bounces-at-nylxs.com Thu Jan 26 18:49:56 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 17:38:28 -0600
Subject: Re: Felsenstein Phylogenies
From: John Harshman
Date: Thu, 26 Jan 2017 15:38:27 -0800
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Xref: panix sci.bio.paleontology:67130
On 1/26/17 2:11 PM, Ruben Safir wrote:
> 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.
Neighbors are trees one transformation away from the original tree. The
number of subtrees not containing that branch is a factor in the
calculation of neighbors below.
>>> 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.
> 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 :(
If you have mathematicians and Comp Sci people to consult, why aren't
there any systematists you can consult? But I have no idea why those
folks don't understand the formula. It seems simple enough to me. The
first term is the number of terminal branches times the number of
subtrees that could be pruned and regrafted to that branch. The second
term is the number of internal branches times the number of subtrees
that could be pruned and regrafted to that branch.
>>> 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.
> the sentence is devoid of specific meaning and is contra to what he just
How so? TBR is not SPR is not NNI. A tree has a different number of
neighbors depending on which transformation you perform.
>> 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.
Let me suggest that the problem is in your comprehension, not in his
text. You need to find some better mathematicians.
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