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,
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
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 "=".
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 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
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,
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
,] -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
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
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
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
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