MESSAGE
DATE  20170126 
FROM  Ruben Safir

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

From learnbouncesatnylxs.com Thu Jan 26 18:49:55 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 C136E161312; Thu, 26 Jan 2017 18:49:54 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 3F43C161311 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 CA49D138AF for ; Thu, 26 Jan 2017 18:49:50 0500 (EST) Received: by panix2.panix.com (Postfix, from userid 20529) id 70B3833CC8; 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: <20170126234950.70B3833CC8atpanix2.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!notformail 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 Lines: 98 MessageID: References: <429a9d551da8b06800494029944f897catmrbrklyn.com> NNTPPostingHost: panix2.panix.com XTrace: reader1.panix.com 1485468691 10914 166.84.1.2 (26 Jan 2017 22:11:31 GMT) XComplaintsTo: abuseatpanix.com NNTPPostingDate: Thu, 26 Jan 2017 22:11:31 +0000 (UTC) UserAgent: tin/2.2.120140504 ("Tober an Righ") (UNIX) (NetBSD/7.0.2 (i386)) 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 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.
> >> 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 :(
>> 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. > 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  _______________________________________________ Learn mailing list Learnatnylxs.com http://lists.mrbrklyn.com/mailman/listinfo/learn

