[R-sig-phylo] phyml executable version 3.0.1 and higher whichve been tested with phymltest

Anna Kostikova anna.kostikova at gmail.com
Tue Feb 2 01:51:27 CET 2010


Dear Emmanuel,

Thanks a lot for your reply. In fact, last week Leonor Palmeira has
sent me a version of Phyml from the binary compiled within Seaview and
that one has worked. So, the problem was really in the Phyml version.
I've also contacted Stephane Guindon who has provided a link to the
Phyml latest binaries.
I'll ask him whether I can post the link to a new website here. But
generally speaking, .exe with Seaview works well.

Thanks again!
Anna

2010/2/1 Emmanuel Paradis <Emmanuel.Paradis at mpl.ird.fr>:
> Hi Anna,
>
> Anna Kostikova wrote on 29/01/2010 12:57:
>>
>> Dear list members,
>>
>> I've been trying to connect R-ape library and phyml executable with
>> "phymltest" function, but presumably due to the fact that I am usuing
>> older version of phyml than 3.0.1, I keep getting following error
>> message (v.3.0):
>> Error in file(con, "r") : unable to open connection.
>> Could anyone who has a Phyml executable tested on compatibility with R
>> send it to me?
>
> I think you should check all options, names of files, and their paths. You
> can try (assuming you use a Mac):
>
> phymltest(....., execname = "/path/to/phyml/phyml_3.0.1_macintel")
>
> An alternative is to create a link to the PhyML executable file and place it
> in the working directory (where you should also place your sequence file).
>
> HTH
>
> Emmanuel
>
>> I am very grateful for your help in advance,
>>
>> Best regards,
>> Anna Kostikova
>>
>> Department of Ecology and Evolution
>> University of Lausanne
>> 1015 Lausanne
>> Switzerland
>>
>> _______________________________________________
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>> R-sig-phylo at r-project.org
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>>
>
> --
> Emmanuel Paradis
> IRD, Montpellier, France
>  ph: +33 (0)4 67 16 64 47
>  fax: +33 (0)4 67 16 64 40
> http://ape.mpl.ird.fr/
>



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