No, unfortunately not. It works perfectly fine with other kinds of files.
Everything, but these ones...The program that generates them does not have
any helpful specifications regarding this format ..*.trees

On Mon, Jun 20, 2011 at 5:55 AM, Bhoom [via R] <
ml-node+3610421-1897267921-239663@n4.nabble.com> wrote:

> Does read.nexus work for you?
>
> Bhoom
>
> On Sun, Jun 19, 2011 at 5:04 PM, Andra Tolbus <[hidden email]<http://user/SendEmail.jtp?type=node&node=3610421&i=0>>wrote:
>
>
> > Dear all,
> >
> >      I am trying to create a consensus skyline plot using the "ape"
> > package(newbie).
> >      I have a nexus file that looks like the one from above containing
> many
> > trees.  (my_file.trees)
> >
> >  #NEXUS
> > begin trees;  [Treefile generated by sim_coal.exe (Laurent Excoffier)]
> >
> > tree true_tree_1 = [&U] (((13.1:6, 43.1:5):12, 28.1:14):284, (((((21.1:0,
>
> > (20.1:1, 4.1:0):0):1, ((37.1:0, (23.1:0, 29.1:0):0):0, 15.1:0):3):7,
> > (36.1:3, (40.1:0, 26.1:1):2):1):2, ((16.1:0, 33.1:0):3, (10.1:0,
> > 18.1:0):2):8):46, ((((6.1:1, (11.1:0, 34.1:0):0):2, 2.1:1):19, (((38.1:4,
>
> > (35.1:4, ((8.1:0, 42.1:0):1, 22.1:0):3):2):0, ((5.1:2, (27.1:0,
> > 39.1:0):0):0, (17.1:0, 30.1:0):1):4):8, ((31.1:0, ((41.1:0, (7.1:0,
> > 25.1:1):0):0, 3.1:0):3):0, (12.1:0, (14.1:0, 1.1:0):0):0):13):10):14,
> > (((24.1:0, 9.1:0):0, 32.1:0):1, 19.1:0):25):20):206);
> > tree true_tree_2 = [&U] ((((37.1:4, ((36.1:0, 25.1:0):0, 39.1:0):2):0,
> > 33.1:1):2, (1.1:0, 43.1:0):1):81, (((((21.1:1, (38.1:1, 14.1:1):0):3,
> > (((29.1:0, 35.1:0):1, 4.1:1):1, ((41.1:1, (24.1:0, ((8.1:0, 32.1:0):0,
> > 7.1:0):0):1):0, (10.1:2, (6.1:1, (26.1:1, (15.1:0,
> > 16.1:0):0):0):0):2):0):4):1, (28.1:1, (3.1:1, 13.1:0):0):7):12,
> (((22.1:5,
> > (((2.1:1, 34.1:1):0, 19.1:0):3, (18.1:0, 42.1:0):3):0):0, 17.1:0):3,
> > (27.1:14, (((30.1:0, 23.1:0):1, 31.1:0):1, 5.1:2):5):3):5):9, ((11.1:0,
> > 9.1:1):0, (12.1:0, (20.1:0, 40.1:1):1):3):23):67);
> >
> > I haven't managed to read this file content using the *read.tree*
> function
> > ..
> >
> >  Error in if (tp[3] != "") obj$node.label <- tp[3] :
> >  missing value where TRUE/FALSE needed
> >
> > Does anyone know first of all, why I cannot read this file (not even with
>
> > read.nexus function)? And secondly how can one generate an "average"
> > skyline
> > plot from several trees?
> >
> > Thank you in advance!
> > Cheers!
> >
> >        [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] <http://user/SendEmail.jtp?type=node&node=3610421&i=1>mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] <http://user/SendEmail.jtp?type=node&node=3610421&i=2>mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
> ------------------------------
>  If you reply to this email, your message will be added to the discussion
> below:
>
> http://r.789695.n4.nabble.com/Skyline-plots-from-several-trees-in-newick-format-tp3609929p3610421.html
>  To unsubscribe from Skyline plots from several trees in newick format, click
> here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=3609929&code=YW5kcmFsaWEudG9sYnVzQGdtYWlsLmNvbXwzNjA5OTI5fC0yMTEyNjI2Njc2>.
>
>


--
View this message in context: http://r.789695.n4.nabble.com/Skyline-plots-from-several-trees-in-newick-format-tp3609929p3610452.html
Sent from the R help mailing list archive at Nabble.com.
	[[alternative HTML version deleted]]

