The complexity of new methodologies can present a challenging barrier towards their uptake. Recognising this, Jeff Powell, author of Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data, has put together an excellent tutorial to guide people through the implementation of his objective, theory-based method for predicting species boundaries, which explicitly incorporates uncertainty in the classification system into biodiversity estimation.
The tutorial is available to view and download from Slideshare, and the relevant R code can be found as supplementary material on Wiley Online Library.
.
Methods Blog 
Important comment for people not really into R: on slide 11, for reading tree from file you should use the commands
>tree=read.tree(‘treefile.phylo’)
or for NEXUS format
>tree=read.nexus(‘treefile.nex’)
then ‘tree’ will be the name of the object with the tree information. Use this name for further operations, e.g.
>plot(tree)
Hi,
When I wrote these comands
> library(splits)
> tree=read.nexus(“Danilonex.nex”)
> plot(tree)
> ltt.plot(tree,log=”y”)
everything is ok, but after it I cannot run the GMYC, because it show up the following:
> gmyc(tree, method=”single”, interval=c(0, 10))
Error in gmyc(tree, method = “single”, interval = c(0, 10)) :
Your ultrametric tree is not ultrametric, please check
So I wonder how can I fix it. I already got this ultrameric tree from the software BEAST, but I how can i got the “.tr” to be read for R.
I look forward to hearing from you soon.
Thanks in advance for your help