MESSAGE
DATE  20170126 
FROM  Ruben Safir

SUBJECT  Subject: [Learn] (fwd) Re: Felsenstein Phylogenies

From learnbouncesatnylxs.com Thu Jan 26 18:49:56 2017 ReturnPath: XOriginalTo: archiveatmrbrklyn.com DeliveredTo: archiveatmrbrklyn.com Received: from www.mrbrklyn.com (www.mrbrklyn.com [96.57.23.82]) by mrbrklyn.com (Postfix) with ESMTP id 1FB7F161319; Thu, 26 Jan 2017 18:49:56 0500 (EST) XOriginalTo: learnatnylxs.com DeliveredTo: learnatnylxs.com Received: from mailbackend.panix.com (mailbackend.panix.com [166.84.1.89]) by mrbrklyn.com (Postfix) with ESMTP id 34957160E77 for ; Thu, 26 Jan 2017 18:49:51 0500 (EST) Received: from panix2.panix.com (panix2.panix.com [166.84.1.2]) by mailbackend.panix.com (Postfix) with ESMTP id AAF5E138AB for ; Thu, 26 Jan 2017 18:49:50 0500 (EST) Received: by panix2.panix.com (Postfix, from userid 20529) id 7D2D733CCA; Thu, 26 Jan 2017 18:49:50 0500 (EST) From: Ruben Safir To: learnatnylxs.com UserAgent: tin/2.2.120140504 ("Tober an Righ") (UNIX) (NetBSD/7.0.2 (i386)) MessageId: <20170126234950.7D2D733CCAatpanix2.panix.com> Date: Thu, 26 Jan 2017 18:49:50 0500 (EST) Subject: [Learn] (fwd) Re: Felsenstein Phylogenies XBeenThere: learnatnylxs.com XMailmanVersion: 2.1.17 Precedence: list ListId: ListUnsubscribe: , ListArchive: ListPost: ListHelp: ListSubscribe: , MIMEVersion: 1.0 ContentType: text/plain; charset="usascii" ContentTransferEncoding: 7bit ErrorsTo: learnbouncesatnylxs.com Sender: "Learn"
 forwarded message  Path: reader1.panix.com!panix!bloombeacon.mit.edu!bloombeacon.mit.edu!newsswitch.lcs.mit.edu!ottixnews.ottix.net!border1.nntp.dca1.giganews.com!nntp.giganews.com!buffer1.nntp.dca1.giganews.com!buffer2.nntp.dca1.giganews.com!news.giganews.com.POSTED!notformail NNTPPostingDate: Thu, 26 Jan 2017 17:38:28 0600 Subject: Re: Felsenstein Phylogenies Newsgroups: sci.bio.paleontology References: <429a9d551da8b06800494029944f897catmrbrklyn.com> From: John Harshman Date: Thu, 26 Jan 2017 15:38:27 0800 UserAgent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:45.0) Gecko/20100101 Thunderbird/45.6.0 MIMEVersion: 1.0 InReplyTo: ContentType: text/plain; charset=windows1252; format=flowed ContentTransferEncoding: 7bit MessageID: Lines: 113 XUsenetProvider: http://www.giganews.com XTrace: sv3Y8H95a0O77+pQInooO1wpy3lLSHRLNTzLY7EVENfRBHsJX90HuAc06yLO+yNk30Ujg3nIKWZ4QlNqZx!Z7jniNjAHDoAZjouWLZCyimIT4MVzhyoVVDr0WT4nMJFuvfUxSYIXOVxyjiU3PSI7YR+PyEMM1Yf XComplaintsTo: abuseatgiganews.com XDMCANotifications: http://www.giganews.com/info/dmca.html XAbuseandDMCAInfo: Please be sure to forward a copy of ALL headers XAbuseandDMCAInfo: Otherwise we will be unable to process your complaint properly XPostfilter: 1.3.40 XOriginalBytes: 6006 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 2n3  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 >>> (2n131) + (2n231 ) = (2n31) = 2n8 >>> 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 2n6. >>> 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 2n6 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 n3 interior branches, the total number of neighbors examined by SPR >>> will be >>> >>> n(2n6)+(n+3)(2n8)" >>> >>> That is where he lost me. >> >> Why? Did his formula have n+3 when it should have had n3? 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(n3)=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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