Hello everyone,
Newbie here. I'm looking for a way to generate random trees of N tips,
allowing multifurcations. My N would be 12, so it wouldn't be practical
(nor possible) to work with all the possible trees (cf. allFurcTrees). I'd
be happy with a set of 1000 trees, sampled equiprobably. I'd
algorithm for which this is based is also
discussed in detail in Chapter 3 of my book.
Joe
On Mon, Dec 23, 2013 at 8:57 PM, Eduardo Ascarrunz ear...@gmail.comwrote:
Hi Liam,
Thank you! That looks clever. How does this method bias the sampling? I
think it could be useful for test running
Thanks Joe!
On 24 December 2013 17:31, Joe Felsenstein felse...@uw.edu wrote:
Eduardo Ascarrunz ear...@gmail.com wrote:
Also, I figured out I could work with unrooted trees. I suspect the
procedure would be similar to your rooted method, wouldn't it?
There is a 1-1 correspondence between
,] -3.687637e-05 3.313087e-02
[20,] -7.472282e-04 2.993891e-02
[21,] 2.578922e-04 -8.326114e-04
[22,] -6.027869e-05 8.365089e-04
[23,] -3.776347e-04 1.439056e-02
[24,] -9.808602e-05 3.201904e-02
On 25 December 2013 18:21, Eduardo Ascarrunz ear...@gmail.com wrote:
Thanks Joe!
On 24 December 2013 17
Please ignore my last message, it was sent by mistake. Sorry!
Happy new year to all.
E.
On 2 January 2014 11:41, Eduardo Ascarrunz ear...@gmail.com wrote:
alloreg2-c(1:48)
dim(alloreg2)-c(nrow=24,ncol=2)
for (i in 2:25) {
+
alloreg2[i-1,]-c(summary((lm(datasetln[,i]~datasetln[,1
Hello Chris,
I know there's a program that was specifically developed for calculating
large pairwise Robinson-Foulds distances matrices efficiently. I'll be able
to send you the reference this evening (Paris time).
All the best,
E.
On 14 Apr 2014 14:44, Chris Buddenhagen cbuddenha...@gmail.com
Hi,
It's not clear from your code how are you using `fixdata` in your
analysis. Is `SWSPeak` a vector you are extracting from the `fixdata`
table? Could it be that you still have the old (w/o species removed)
`SWSPeak` in memory from a previous session?
Best,
E.
On 5 January 2016 at 07:50,
Hi Chris,
The tntfile2R and tntfile2newick functions from Nick Matzke's package TNTR
should help you with that. Here's the link:
http://phylo.wdfiles.com/local--files/tntr/tnt_R_utils_v1.R
You can also export files in Newick format directly from TNT using the
command EXPORT with the flag "=".
Hi Ting-Wen.
Are you using the latest version of ape? Emmanuel released ape v.4.0
yesterday with a bug fix for that function.
Best,
Eduardo
2016-11-11 0:35 GMT+01:00 Chen, Ting-Wen <
ting-wen.c...@biologie.uni-goettingen.de>:
> Dear all,
>
> recently I got an error when downloading sequences
read.GenBank() uses HTTPS in place of HTTP. The relevant information from
> NCBI can be found there:
>
> https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/
>
> Best,
>
> Emmanuel
>
>
> Le 11/11/2016 à 09:22, Eduardo Ascarrunz a écrit :
>
>> Hi Ti
Hi Jesse,
Do you want to select the trees that are most incongruent with some sort of
average of the tree distribution? The `treespace`and `phytools` packages
have functions that compute average trees with different metrics, and they
also allow you to measure the distance between each tree and
Maybe you could use a birth-death model. You can estimate the speciation
rate and extinction rate from your original tree, and use those parameters
to run simulations of trees for 5 My with the pbtree function from
phytools. Run as many simulations as you have living tips in your original
tree,
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