MESSAGE
| DATE | 2017-01-26 |
| FROM | Ruben Safir
|
| SUBJECT | Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
|
From learn-bounces-at-nylxs.com Thu Jan 26 18:50:17 2017
Return-Path:
X-Original-To: archive-at-mrbrklyn.com
Delivered-To: archive-at-mrbrklyn.com
Received: from www.mrbrklyn.com (www.mrbrklyn.com [96.57.23.82])
by mrbrklyn.com (Postfix) with ESMTP id D801716131A;
Thu, 26 Jan 2017 18:50:16 -0500 (EST)
X-Original-To: learn-at-nylxs.com
Delivered-To: learn-at-nylxs.com
Received: from mailbackend.panix.com (mailbackend.panix.com [166.84.1.89])
by mrbrklyn.com (Postfix) with ESMTP id 6EC50161317
for ; Thu, 26 Jan 2017 18:49:52 -0500 (EST)
Received: from panix2.panix.com (panix2.panix.com [166.84.1.2])
by mailbackend.panix.com (Postfix) with ESMTP id EA3AD138B3
for ; Thu, 26 Jan 2017 18:49:50 -0500 (EST)
Received: by panix2.panix.com (Postfix, from userid 20529)
id 3C94E33CC5; Thu, 26 Jan 2017 18:49:50 -0500 (EST)
From: Ruben Safir
To: learn-at-nylxs.com
User-Agent: tin/2.2.1-20140504 ("Tober an Righ") (UNIX) (NetBSD/7.0.2 (i386))
Message-Id: <20170126234950.3C94E33CC5-at-panix2.panix.com>
Date: Thu, 26 Jan 2017 18:49:50 -0500 (EST)
Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
X-BeenThere: learn-at-nylxs.com
X-Mailman-Version: 2.1.17
Precedence: list
List-Id:
List-Unsubscribe: ,
List-Archive:
List-Post:
List-Help:
List-Subscribe: ,
MIME-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
Content-Transfer-Encoding: 7bit
Errors-To: learn-bounces-at-nylxs.com
Sender: "Learn"
-- 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 06:46:40 -0500
Organization: PANIX Public Access Internet and UNIX, NYC
Lines: 61
Message-ID: <429a9d55-1da8-b068-0049-4029944f897c-at-mrbrklyn.com>
References:
NNTP-Posting-Host: www.mrbrklyn.com
Mime-Version: 1.0
Content-Type: text/plain; charset=windows-1252
Content-Transfer-Encoding: 7bit
X-Trace: reader1.panix.com 1485431200 12715 96.57.23.82 (26 Jan 2017 11:46:40 GMT)
X-Complaints-To: abuse-at-panix.com
NNTP-Posting-Date: Thu, 26 Jan 2017 11:46:40 +0000 (UTC)
To: "learn-at-nylxs.com"
User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101
Thunderbird/45.5.1
In-Reply-To:
Xref: panix sci.bio.paleontology:67125
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.
I guess that is all the possible combinations assuming the same
attachment locations for the trees, examining one tree at a time.
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?
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. 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"
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?
:)
-- end of forwarded message --
_______________________________________________
Learn mailing list
Learn-at-nylxs.com
http://lists.mrbrklyn.com/mailman/listinfo/learn
|
|
