Sun Jan 29 11:33:03 2023
EVENTS
 FREE
SOFTWARE
INSTITUTE

POLITICS
JOBS
MEMBERS'
CORNER

MAILING
LIST

NYLXS Mailing Lists and Archives
NYLXS Members have a lot to say and share but we don't keep many secrets. Join the Hangout Mailing List and say your peice.

DATE 2017-01-01

LEARN

2023-01-29 | 2022-12-29 | 2022-11-29 | 2022-10-29 | 2022-09-29 | 2022-08-29 | 2022-07-29 | 2022-06-29 | 2022-05-29 | 2022-04-29 | 2022-03-29 | 2022-02-28 | 2022-01-28 | 2021-12-28 | 2021-11-28 | 2021-10-28 | 2021-09-28 | 2021-08-28 | 2021-07-28 | 2021-06-28 | 2021-05-28 | 2021-04-28 | 2021-03-28 | 2021-02-28 | 2021-01-28 | 2020-12-28 | 2020-11-28 | 2020-10-28 | 2020-09-28 | 2020-08-28 | 2020-07-28 | 2020-06-28 | 2020-05-28 | 2020-04-28 | 2020-03-28 | 2020-02-28 | 2020-01-28 | 2019-12-28 | 2019-11-28 | 2019-10-28 | 2019-09-28 | 2019-08-28 | 2019-07-28 | 2019-06-28 | 2019-05-28 | 2019-04-28 | 2019-03-28 | 2019-02-28 | 2019-01-28 | 2018-12-28 | 2018-11-28 | 2018-10-28 | 2018-09-28 | 2018-08-28 | 2018-07-28 | 2018-06-28 | 2018-05-28 | 2018-04-28 | 2018-03-28 | 2018-02-28 | 2018-01-28 | 2017-12-28 | 2017-11-28 | 2017-10-28 | 2017-09-28 | 2017-08-28 | 2017-07-28 | 2017-06-28 | 2017-05-28 | 2017-04-28 | 2017-03-28 | 2017-02-28 | 2017-01-28 | 2016-12-28 | 2016-11-28 | 2016-10-28 | 2016-09-28 | 2016-08-28 | 2016-07-28 | 2016-06-28 | 2016-05-28 | 2016-04-28 | 2016-03-28 | 2016-02-28 | 2016-01-28 | 2015-12-28 | 2015-11-28 | 2015-10-28 | 2015-09-28 | 2015-08-28 | 2015-07-28 | 2015-06-28 | 2015-05-28 | 2015-04-28 | 2015-03-28 | 2015-02-28 | 2015-01-28 | 2014-12-28 | 2014-11-28 | 2014-10-28

Key: Value:

Key: Value:

MESSAGE
DATE 2017-01-26
FROM Ruben Safir
SUBJECT Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
From learn-bounces-at-nylxs.com Thu Jan 26 18:50:19 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 EC4EC16131B;
Thu, 26 Jan 2017 18:50:18 -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 6A721161315
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 2C324138B6
for ; Thu, 26 Jan 2017 18:49:50 -0500 (EST)
Received: by panix2.panix.com (Postfix, from userid 20529)
id 6518033CC7; 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: <20170126234950.6518033CC7-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!bloom-beacon.mit.edu!bloom-beacon.mit.edu!168.235.88.217.MISMATCH!feeder.erje.net!2.us.feeder.erje.net!feeder.usenetexpress.com!feeder1.iad1.usenetexpress.com!216.166.98.84.MISMATCH!border1.nntp.dca1.giganews.com!border2.nntp.dca1.giganews.com!nntp.giganews.com!buffer2.nntp.dca1.giganews.com!news.giganews.com.POSTED!not-for-mail
NNTP-Posting-Date: Thu, 26 Jan 2017 10:56:45 -0600
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 08:56:45 -0800
User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:45.0)
Gecko/20100101 Thunderbird/45.6.0
MIME-Version: 1.0
In-Reply-To: <429a9d55-1da8-b068-0049-4029944f897c-at-mrbrklyn.com>
Content-Type: text/plain; charset=windows-1252; format=flowed
Content-Transfer-Encoding: 7bit
Message-ID:
Lines: 80
X-Usenet-Provider: http://www.giganews.com
X-Trace: sv3-6N1BtAi0GtL9xFoAEdQ5dyYBUJwBnQGSBJGFnimSxO082lAFdze6JFfeGPyIp8df4YMkBVzNfAJkwqt!yjZKodV1Kpyb2by4cFGht/qWAXeufhwTOUxj7p+J68vKkyuHPZbcm/ywZIM0j/DKAyEt5Ll8ejA/
X-Complaints-To: abuse-at-giganews.com
X-DMCA-Notifications: http://www.giganews.com/info/dmca.html
X-Abuse-and-DMCA-Info: Please be sure to forward a copy of ALL headers
X-Abuse-and-DMCA-Info: Otherwise we will be unable to process your complaint properly
X-Postfilter: 1.3.40
Bytes: 4288
X-Original-Bytes: 4226
Xref: panix sci.bio.paleontology:67128

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.

> 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.

> 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.

For all of these, you need to explain what you think the problem is.


-- end of forwarded message --
_______________________________________________
Learn mailing list
Learn-at-nylxs.com
http://lists.mrbrklyn.com/mailman/listinfo/learn

  1. 2017-01-09 James E Keenan <jkeen-at-verizon.net> Subject: [Learn] Perl Conference 2017: June 18-23: Call for Proposals
  2. 2017-01-09 From: "David H. Adler" <dha-at-panix.com> Subject: [Learn] [MEETING] New year, new meetings.
  3. 2017-01-10 IEEE Engineering in Medicine and Biology Society <noreply-at-embs.org> Subject: [Learn] BHI 2017 -Important Reminders
  4. 2017-01-12 mrbrklyn <mrbrklyn-at-panix.com> Subject: [Learn] Fwd: [Accu-contacts] C/C++ Engineer Roles - YouView set-top
  5. 2017-01-16 mrbrklyn <mrbrklyn-at-panix.com> Subject: [Learn] openscience this year
  6. 2017-01-19 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] (fwd) Re: Keith Hernandez should be coaching,
  7. 2017-01-19 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Keith Hernandez should be coaching,
  8. 2017-01-19 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Keith Hernandez should be coaching,
  9. 2017-01-19 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Keith Hernandez should be coaching,
  10. 2017-01-19 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Keith Hernandez should be coaching,
  11. 2017-01-19 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Keith Hernandez should be coaching,
  12. 2017-01-19 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Keith Hernandez should be coaching,
  13. 2017-01-19 Rick Moen <rick-at-linuxmafia.com> Subject: [Learn] [Hangout-NYLXS] RAM and RAM-testing
  14. 2017-01-19 Rick Moen <rick-at-linuxmafia.com> Subject: [Learn] [Hangout-NYLXS] RAM and RAM-testing
  15. 2017-01-20 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Follow up conversation
  16. 2017-01-20 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fwd: cs691 notes and task
  17. 2017-01-20 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Alumni Publications
  18. 2017-01-20 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] Follow up conversation
  19. 2017-01-20 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: threads and exit() woes
  20. 2017-01-20 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: threads and exit() woes
  21. 2017-01-21 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: Re: Nueral Networks
  22. 2017-01-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Nice project to learn from
  23. 2017-01-23 IEEE Engineering in Medicine and Biology Society <noreply-at-embs.org> Subject: [Learn] 8th International IEEE EMBS Conference on Neural
  24. 2017-01-23 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] anyone understand this - ME
  25. 2017-01-23 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] compiler job
  26. 2017-01-23 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: Nueral Networks
  27. 2017-01-23 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Parse Tree theory
  28. 2017-01-24 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Computational evolution
  29. 2017-01-25 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Felsenstein Phylogenies
  30. 2017-01-25 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] R Programming Workshop
  31. 2017-01-26 ruben safir <ruben-at-mrbrklyn.com> Re: [Learn] Felsenstein Phylogenies
  32. 2017-01-26 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] [Hangout-NYLXS] librepalnet
  33. 2017-01-26 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Felsenstein Phylogenies
  34. 2017-01-26 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
  35. 2017-01-26 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
  36. 2017-01-26 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
  37. 2017-01-26 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
  38. 2017-01-26 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
  39. 2017-01-26 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
  40. 2017-01-26 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
  41. 2017-01-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Installfest at LIU Brooklyn
  42. 2017-01-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] librepalnet
  43. 2017-01-27 Christopher League <league-at-contrapunctus.net> Subject: [Learn] P vs NP
  44. 2017-01-28 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] P vs NP
  45. 2017-01-28 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: Felsenstein Phylogenies
  46. 2017-01-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] R Programming Workshop
  47. 2017-01-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] R workshop
  48. 2017-01-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] [Hangout-NYLXS] Installfest for Lunch
  49. 2017-01-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] [ruben-at-mrbrklyn.com: [Hangout-NYLXS] Installfest for Lunch]
  50. 2017-01-31 ruben <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [dinosaur] Collagen preserved in Early Jurassic
  51. 2017-01-31 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [isoc-ny] FCC Seeks Diverse Stakeholders for Broadband

NYLXS are Do'ers and the first step of Doing is Joining! Join NYLXS and make a difference in your community today!