Dear all, I'm trying to do a whole-genome maximum likelihood tree on the concatenated alignment of all genes. I used the package phangorn to construct a pml object, and tries to do an optimization using optim.pml :
ml.pml <- pml(tree2,test.phyDat) ml.optim <- optim.pml(ml.pml,model="K80",optNni=T,optEdge=T) I can't give you the tree as the alignment file is about 30 Mb and the dput doesn't fit on the R screen... Is there an obvious reason for this error, and is there a solution you can think of? Maybe there's a better way of getting a maximum likelihood tree from such an alignment? I tried Phylip and FastTree, but both run out of memory on my 4Gb 32-bit system. Cheers Joris -- Joris Meys Statistical Consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control Coupure Links 653 B-9000 Gent tel : +32 9 264 59 87 [email protected] ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
