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Agus Camacho | 23 May 03:54
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Zero value of a significant model parameter during PGLS

Dear all,

I just had the following result fitting a Pgls with both, brownian and O-U
correlation structures.
I was wandering what could have made the value and Sd go to zero. Altitude
values were considered continuous but were strongly grouped in two levels.
Might that have to do with the result?

Would appreciate any hint.
There goes the model's summary.
Thanks in advance.

Generalized least squares fit by maximum likelihood
  Model: temperature ~ 1 + altitude
  Data: tp
  AIC BIC logLik
   60  62    -26

Correlation Structure: corMartins
 Formula: ~1
 Parameter estimate(s):
alpha
   21

Coefficients:
            Value Std.Error t-value p-value
(Intercept)    35       2.8    12.7   0.000
altitude        0       0.0    -2.2   0.057

 Correlation:
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Klaus Schliep | 22 May 12:28
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Re: center of tree

Hello Mathias,

I'm not aware of any general  COT in R, your chance to make a contribution.
Midpoint rooting is the COT for a special function F [2], it minimizes
the maximum
distance from the root (COT) to the tips.

Cheers,
Klaus

On 5/18/12, Walter, Mathias <mathias@...> wrote:
> Hi,
>
> does anyone know a package which computes the center of a tree (COT)?
>
> The COT is a point on an unrooted phylogeny, where the average
> evolutionary distance from this point to each tip on the phylogeny is
> minimized [1,2].
>
> Once I thought this COT is identical with the midpoint used to root a
> tree. But I'm unsure.
>
>
> [1] http://www.sciencemag.org/content/299/5612/1515.3
> [2] http://jvi.asm.org/content/81/16/8507
>
> --
> Regards,
> Mathias
>
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Juan Antonio Balbuena | 22 May 11:49
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compute HKY85 distances in R

Hello
I would like to know whether it is possible to compute HKY85 genetic
distances using R. The model is not included in the dist.dna function
of ape and I was wondering whether it is available in another package.
Thank you very much for your attention.

Juan Antonio Balbuena
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Emmanuel Paradis | 18 May 13:34
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Re: unrooted tree, spread tips

Walter, Mathias wrote on 18/05/2012 18:16:
> Hi,
>
> if I use type="r", then quite a lot of lines cross.

This should not happen. May be a bug. You have an example of this?

E.

> I tried optimal
> tree ordering but as soon as I convert my hclust object to a phylo
> object (via as.phylo), the ordering is lost.
>
> Another advantage of the unrooted tree is, that you can often clearly
> distinguish main clusters. That is not possible with any other kind of
> tree drawing.
>
> --
> Kind regards,
> Mathias
>
> 2012/5/18 Emmanuel Paradis<Emmanuel.Paradis@...>:
>> Hi,
>>
>> Walter, Mathias wrote on 18/05/2012 16:42:
>>
>>> Hi,
>>>
>>> I use ape to plot my phylogenetic trees. Often I have to plot unrooted
>>> trees with few clades, but a lot of tips per clade. The tip labels are
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Walter, Mathias | 18 May 13:16

Re: unrooted tree, spread tips

Hi,

if I use type="r", then quite a lot of lines cross. I tried optimal
tree ordering but as soon as I convert my hclust object to a phylo
object (via as.phylo), the ordering is lost.

Another advantage of the unrooted tree is, that you can often clearly
distinguish main clusters. That is not possible with any other kind of
tree drawing.

--
Kind regards,
Mathias

2012/5/18 Emmanuel Paradis <Emmanuel.Paradis@...>:
> Hi,
>
> Walter, Mathias wrote on 18/05/2012 16:42:
>
>> Hi,
>>
>> I use ape to plot my phylogenetic trees. Often I have to plot unrooted
>> trees with few clades, but a lot of tips per clade. The tip labels are
>> hard to read, even if I use lab4ut="axial". Is there any way to spread
>> the tips?
>
>
> No. The only available algorithm for unrooted trees in ape is the
> "equal-angle" one. It seems that for your purpose type="r" might be not bad,
> even though the center of the circle is the root.
(Continue reading)

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Emmanuel Paradis | 18 May 12:53
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Re: unrooted tree, spread tips

Hi,

Walter, Mathias wrote on 18/05/2012 16:42:
> Hi,
>
> I use ape to plot my phylogenetic trees. Often I have to plot unrooted
> trees with few clades, but a lot of tips per clade. The tip labels are
> hard to read, even if I use lab4ut="axial". Is there any way to spread
> the tips?

No. The only available algorithm for unrooted trees in ape is the 
"equal-angle" one. It seems that for your purpose type="r" might be not 
bad, even though the center of the circle is the root.

Best,

Emmanuel

> I saw this in some other tree drawing programs.
>
> Kind regards,
> Mathias
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Walter, Mathias | 18 May 11:42

unrooted tree, spread tips

Hi,

I use ape to plot my phylogenetic trees. Often I have to plot unrooted
trees with few clades, but a lot of tips per clade. The tip labels are
hard to read, even if I use lab4ut="axial". Is there any way to spread
the tips? I saw this in some other tree drawing programs.

--
Kind regards,
Mathias
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Hilmar Lapp | 16 May 20:18
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Mentorship program the 2012 iEvoBio conference

The iEvoBio Mentorship Program pairs undergraduate and graduate students with faculty who have
extensive experience in evolution, systematics, biodiversity, mathematics and/or software
development to enhance their experience at iEvoBio 2012. Mentors will guide participants in
collaborative and networking opportunities throughout the two-day conference.

If you would like to gain the wisdom of your colleagues' experiences by participating in this program,
please email the iEvoBio 2012 organizing committee at
committee@... by June 1, indicating if you have any activities
you would like to be included in the mentorship program, or a particular field of interest. You can find
more information about the meeting and registration at http://ievobio.org/.

iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters
Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB).

The iEvoBio 2012 Organizing Committee:
Hilmar Lapp, US National Evolutionary Synthesis Center (chair)
Robert Beiko, Dalhousie University
Nico Cellinese, University of Florida
Robert Guralnick, University of Colorado at Boulder
Rebecca Kao, Denver Botanic Gardens
Ellinor Michel, Natural History Museum, London
Nadia Talent, Royal Ontario Museum
Andrea Thomer, University of Illinois at Urbana-Champaign
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Julien Lorion | 16 May 09:53
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Best way to test correlation between discrete and continuous variables ?

Dear all, 

I am working on the evolution of deep-sea symbiotic mussels... I have got a tree and 5 characters: habitat
(hydrothermal vents, cold seep and organic substrate), presence/absence of methanotrophic
symbionts, presence/absence of sulfoxydizing symbionts, symbiont location (extra VS intracellular)
and body length... 

So that's 1 continuous and 4 discrete binary variables (actually, I assumed vent and seeps are very
similar... so no need to take into account the 3 states) 

At first I tested various hypotheses about correlation between my discrete characters... I chose the easy
way: I remembered my master lectures and used basic Pagel's correlations. If you think that any new tool
performs better, I'd be happy to hear it. 

For now, my main concern is that I wanna test the impact of two binary variables (habitat and symbiont
location) on the body length... In fact, that looks likes ANOVAs from which I wanna remove the
phylogenetic bias... 

The point is that I don't know how to do that in practice. May someone have some advices ?

Thanks by advance

Best regards

Julien
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Emmanuel Paradis | 15 May 12:41
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Re: exporting nexus tree in APE

Hi Lucinda,

You don't give enough information allowing us to help you efficiently. 
However, see below.

Lucinda Kirkpatrick wrote on 15/05/2012 07:38:
> Dear all,
>
> I am attempting to export a tree I have pruned from 916 taxa to the 53 taxa
> I am interested. I used this script:
>
> overlap<- name.check(tree, d)
> tree<- drop.tip(tree, overlap$Tree.not.data)
> d2<- d[!(rownames(d) %in% overlap$Data.not.tree),]
>
>
> plot(tree)
> name.check(tree,d2)
>
> That was successful but now I want to export the reduced tree as a nexus
> file I get the following error:
>
>   write.nexus(tree, file="./Results/Tree.nex")
> Read 921 items

This suggests you use an old version of ape (which reads the original 
data from the NEXUS fil: this feature has been deprecated). I suggest 
you update ape first; if your problem persists give us more details, 
possibly with some example data.
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Emmanuel Paradis | 15 May 12:35
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Re: NaN returned with dist.dna {ape}

Hi Augusto,

If you read my book, you should have met a sentence like "Once an 
alignment has been performed, it is recommended to check its quality by 
visual inspection." In your case, the following command is revealing:

image(sapinhos.seq.ali)

Best,

Emmanuel

Augusto Ribas wrote on 15/05/2012 04:25:
> Hello.
> I'm reading" Analysis of Phylogenetics and Evolution with R" and tryed to
> make a tree with some frogs species repeating the Sylvia Case study example.
> I had no problem in search, download and align many 16s sequences for
> several frog species.
> I used a web service to align the sequences.
> The results are here:
> http://www.ebi.ac.uk/Tools/services/web_clustalw2/toolresult.ebi?tool=clustalw2&jobId=clustalw2-I20120514-220954-0303-43791553-oy
>
> Then i read this align sequences and try to calc the distance, but some NaN
> are returned, not allowing me to continue.
>
> #reading data
> sapinhos.seq.ali<-read.dna("
> http://www.ebi.ac.uk/Tools/services/rest/clustalw2/result/clustalw2-I20120514-220954-0303-43791553-oy/aln-phylip
> ")
> sapinhos.seq.ali
(Continue reading)

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Gmane