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OpenTreeOfLife / hackathon

A repo for the 2014 OpenTree / Arbor / HIP hackathon
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Integrate Open tree of life with species delimitation model. #10

Open maribetg opened 10 years ago

maribetg commented 10 years ago

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.

kcranston commented 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)?

bobthacker commented 10 years ago

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.

bomeara commented 10 years ago

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).