Open maribetg opened 10 years ago
I am not quite sure what you are proposing to implement in Open Tree. Do these methods use a tree as part of their input, or do they produce a tree (or both)?
Can R package 'spider' accomplish the species delimitation tasks that are needed? I am working on incorporating 'spider' into the Arbor framework, but I agree that it would be great to retrieve the starting tree and annotations from OpenTree.
spider and adhoc could both potentially be useful. See http://cran.r-project.org/web/views/Phylogenetics.html for utility of various R packages in phylo (these were the only two listed for species delim; let me know if you know of more).
Now on days, knowing species number and delimitation of species is a essential task for biodiversity purposes and/or conservation issues. It will allow to identify conservation units and endangered species. There are two different models, GMYC model (General Mixed Yule Coalescent model, Pons et al 2006) and PTP model (aPoisson tree Process model, Zhang et a;. 2013) using phylogenetic trees. The first one could be done with a script from R language, and the second one it is done with a script from python code. I want to include both under Open tree of life, so you can easily determinate species number under one program.