Hello, I'm looking for approaches how to get a species tree from set of gene trees. I was looking at Phybase package https://code.google.com/p/phybase/ but it seems to be abandoned and when I tried to install it, I ended up with error: install.packages("~/stazene/phybase_1.3.tar.gz", repos=NULL, type="source") Installing package into ‘/home/vojta/R/x86_64-suse-linux-gnu-library/3.1’ (as ‘lib’ is unspecified) * installing *source* package ‘phybase’ ... ERROR: a 'NAMESPACE' file is required * removing ‘/home/vojta/R/x86_64-suse-linux-gnu-library/3.1/phybase’ Warning in install.packages : installation of package ‘/home/vojta/stazene/phybase_1.3.tar.gz’ had non- zero exit status I'm working on Linux. Well, I have gene trees (in multiPhylo object). I tried superTree, densiTree and speciesTree from phangorn. Those are looking very well, but I'd like to try some coalescence based approach. I was looking at coalSpeciesTree from phangorn, but I don't know how to supply that X phyDat object - my gene trees have all same tips and species are same in all trees. How to define it? Or is there any other better approach how to get species tree out of gene trees? Sincerely, Vojtěch
-- Vojtěch Zeisek http://trapa.cz/en/ Department of Botany, Faculty of Science Charles University in Prague Benátská 2, Prague, 12801, CZ http://botany.natur.cuni.cz/en/ Institute of Botany, Academy of Science Zámek 1, Průhonice, 25243, CZ http://www.ibot.cas.cz/en/ Czech Republic
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