This is easy to do using Bayesian methods. See:
http://www.biomedcentral.com/content/pdf/1471-2148-12-102.pdf
Cheers,
Simon.
On 14/03/13 22:25, Ferguson-Gow, Henry wrote:
Hi
I used the method of Kuhn et al (2011) to resolve polytomies in my tree leaving
me with a posterior of thousands of t
> Date: Thu, 14 Mar 2013 10:21:39 +0100
> From: Gian Maria Niccol? Benucci
> To: r-sig-phylo@r-project.org
> Subject: [R-sig-phylo] How to cluster sequences in different OTUs
>
> Hi everyone,
>
> I was wondering is exist a function that is able to generate OTUs from a
> sequences database.
> Tha
Dear Gian,
Have you looked at the "spider" package? Sequences can be downloaded from
the GenBank or BOLD databases, and OTUs can then be estimated from a
distance matrix using a predefined threshold ("tclust" function), or by a
threshold estimated from the data ("localMinima" function).
If you wa
Hi
I used the method of Kuhn et al (2011) to resolve polytomies in my tree leaving
me with a posterior of thousands of trees. I was wondering how I would go about
using PGLS on a sample of these trees so that the uncertainty in the resolution
of the polytomies is incorporated into my analysis (
Hi everyone,
I was wondering is exist a function that is able to generate OTUs from a
sequences database.
Thank you very much in advance,
--
Gian
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