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 want something more sophisticated, then try the GMYC of Monaghan et
al. (2009), in the "splits" package. This, however, requires you input an
ultrametric tree generated by a program such as BEAST. Having said that, if
you wanted to keep it all in R, then for this purpose consider the ML
functions ("pml" and "optim.pml") in phangorn, and the "chronopl" function
in ape.
Hope this helps.
Message: 1
> Date: Thu, 14 Mar 2013 10:21:39 +0100
> From: Gian Maria Niccol? Benucci <[email protected]>
> To: [email protected]
> Subject: [R-sig-phylo] How to cluster sequences in different OTUs
> Message-ID:
> <CAPxEaEQ2RkdimTWr7uQP3SbLoorqokBcymgA1B6z8u0KV0B=
> [email protected]>
> Content-Type: text/plain
>
> 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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