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DATE 2017-01-01

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MESSAGE
DATE 2017-01-28
FROM ruben safir
SUBJECT Subject: [Learn] Fwd: Re: Felsenstein Phylogenies
From learn-bounces-at-nylxs.com Sat Jan 28 18:48:30 2017
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see how this turns

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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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Xref: panix sci.bio.paleontology:67129

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.

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Subject: Re: Felsenstein Phylogenies
Newsgroups: sci.bio.paleontology
References:

<429a9d55-1da8-b068-0049-4029944f897c-at-mrbrklyn.com>


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
>>>
>>> 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 :(

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
>>> 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.

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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From: ruben safir
Newsgroups: sci.bio.paleontology
Subject: Re: Felsenstein Phylogenies
Date: Fri, 27 Jan 2017 09:42:24 -0500
Organization: PANIX Public Access Internet and UNIX, NYC
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<429a9d55-1da8-b068-0049-4029944f897c-at-mrbrklyn.com>



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On 01/26/2017 06:38 PM, John Harshman wrote:
> 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.


I'm essentially limited to the faculty at LIU/Brooklyn. This text is
not clear in its use of terminology. I think your benefiting from your
years in the field and not seeing how the text is perceived from a comp
sci student. I just don't know what an external branch is. You have
defined within tree theory edges and nodes. Node at the tip of trees
are called leafs. Without specific definitions it is very difficult to
follow what he is counting. And in this chapter, it is easy to show
that areas that require a chapter of discussion are given small
paragraphs. For example, took at Cormen's Introduction to Algorithms
side by side. It is over 1100 pages with a full glossary and index.

> 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.

What is a terminal branch. The diagram he gives show that most of the
nodes are attached to leaves. Why is this multiplication? What
permutation are we describing?

> The second
> term is the number of internal branches times the number of subtrees
> that could be pruned and regrafted to that branch.

In that diagram there is only one?

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NNTP-Posting-Date: Fri, 27 Jan 2017 14:08:14 -0600
Subject: Re: Felsenstein Phylogenies
Newsgroups: sci.bio.paleontology
References:

<429a9d55-1da8-b068-0049-4029944f897c-at-mrbrklyn.com>




From: John Harshman
Date: Fri, 27 Jan 2017 12:08:14 -0800
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On 1/27/17 6:42 AM, ruben safir wrote:
> On 01/26/2017 06:38 PM, John Harshman wrote:
>> 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.
>
>
> I'm essentially limited to the faculty at LIU/Brooklyn.

There are no systematists at LIU/Brooklyn?

> This text is
> not clear in its use of terminology. I think your benefiting from your
> years in the field and not seeing how the text is perceived from a comp
> sci student. I just don't know what an external branch is. You have
> defined within tree theory edges and nodes. Node at the tip of trees
> are called leafs.

Then an external node is a leaf. An external branch is an edge that has
a leaf at one end. All clear now?

> Without specific definitions it is very difficult to
> follow what he is counting. And in this chapter, it is easy to show
> that areas that require a chapter of discussion are given small
> paragraphs. For example, took at Cormen's Introduction to Algorithms
> side by side. It is over 1100 pages with a full glossary and index.

Why are you complaining to me about the book?

>> 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.
>
> What is a terminal branch. The diagram he gives show that most of the
> nodes are attached to leaves. Why is this multiplication? What
> permutation are we describing?

A terminal branch is an external branch is an edge with a leaf at one
end. It's multiplication because for each branch there a certain number
of possible subtrees. Thus the total number of rearrangements is
branches * subtrees, computed separately for terminal and internal branches.

>> The second
>> term is the number of internal branches times the number of subtrees
>> that could be pruned and regrafted to that branch.
>
> In that diagram there is only one?
>
What diagram? Only one what? Is it possible that the mathematicians you
asked about all this also had no idea what you were trying to say?

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From: ruben safir
Newsgroups: sci.bio.paleontology
Subject: Re: Felsenstein Phylogenies
Date: Fri, 27 Jan 2017 17:58:13 -0500
Organization: PANIX Public Access Internet and UNIX, NYC
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References:

<429a9d55-1da8-b068-0049-4029944f897c-at-mrbrklyn.com>





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On 01/27/2017 03:08 PM, John Harshman wrote:
> Why are you complaining to me about the book?

I'm not. I'm just explaing my trouble understanding it.

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Subject: Re: Felsenstein Phylogenies
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<429a9d55-1da8-b068-0049-4029944f897c-at-mrbrklyn.com>






From: John Harshman
Date: Fri, 27 Jan 2017 20:12:34 -0800
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On 1/27/17 2:58 PM, ruben safir wrote:
> On 01/27/2017 03:08 PM, John Harshman wrote:
>> Why are you complaining to me about the book?
>
> I'm not. I'm just explaing my trouble understanding it.
>
So is this helping at all?

I would suggest a change of attitude. If you don't understand something,
don't assume as a first hypothesis that Felsenstein is wrong.

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From: ruben safir
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Subject: Re: Felsenstein Phylogenies
Date: Fri, 27 Jan 2017 23:23:39 -0500
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Xref: panix sci.bio.paleontology:67135

On 01/27/2017 11:12 PM, John Harshman wrote:
>> I'm not. I'm just explaing my trouble understanding it.
>>
> So is this helping at all?
>

Yes, and I thank you for taking the time to give me your insights.


> I would suggest a change of attitude. If you don't understand something,
> don't assume as a first hypothesis that Felsenstein is wrong.

There is nothing wrong with my attitude, and my first assumption is FAR
from assuming the text is wrong, although it is sometimes possible.
That is my last assumption, however, and I have have a couple of
notebooks filled with diagrams and charts trying to determine what the
author means and how his theories works. The editing of the text can be
better, and the text can be better written, but this is increasingly the
case as time goes on. Textbook quality and tech books have fallen badly
in the last decade.

Ruben

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From: Popping mad
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Subject: Re: Felsenstein Phylogenies
Date: Sat, 28 Jan 2017 19:00:58 +0000 (UTC)
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Xref: panix sci.bio.paleontology:67136

On Fri, 27 Jan 2017 12:08:14 -0800, John Harshman wrote:

> A terminal branch is an external branch is an edge with a leaf at one
> end. It's multiplication because for each branch there a certain number
> of possible subtrees. Thus the total number of rearrangements is
> branches * subtrees, computed separately for terminal and internal
> branches.
>
>>> The second term is the number of internal branches times the number of
>>> subtrees that could be pruned and regrafted to that branch.
>>
>> In that diagram there is only one?
>>
> What diagram? Only one what? Is it possible that the mathematicians you
> asked about all this also had no idea what you were trying to say?

The diagram on page 42 that is marched figure 4.5. All the nodes in that
initial tree, when reviewing Subtree pruning and regrafting, seems to
have only one internal node, that is a node that does not attach to a
leaf. This perplexed us greatly.

Ruben

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