MESSAGE
| DATE | 2017-01-26 |
| FROM | Ruben Safir
|
| SUBJECT | Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
|
From learn-bounces-at-nylxs.com Thu Jan 26 18:50:15 2017
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From: Ruben Safir
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Date: Thu, 26 Jan 2017 18:49:50 -0500 (EST)
Subject: [Learn] (fwd) Re: Felsenstein Phylogenies
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NNTP-Posting-Date: Wed, 25 Jan 2017 20:35:33 -0600
Subject: Re: Felsenstein Phylogenies
Newsgroups: sci.bio.paleontology
References:
From: John Harshman
Date: Wed, 25 Jan 2017 18:35:32 -0800
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Xref: panix sci.bio.paleontology:67123
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.
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