Hi John, I don't have a simple solution for this in R (although I'm sure there is one), but we will add this as an output option in PartitionFinder in future releases.
If you have no luck here (the question is a bit off topic for this list), try posting on Stack Overflow. Rob On 4 April 2013 03:12, John Denton <jden...@amnh.org> wrote: > Hi all, > > PartitionFinder selected a complex partitioning scheme that I would like > to put into a TreeFinder analysis. As far as I know, TreeFinder ignores > NEXUS SETS blocks, and so I would have to input the partitioning by hand. I > do this normally for repetitive partitions, e.g. codon positions, but the > partitioning is more tedious in this case: > > charset p1 = 1-373\3, 2-374\3, 3-375\3, 376-958\3, 377-959\3, 378-960\3, > 961-1648\3, 962-1649\3, 1652-2495\3, 2497-3241\3, 2498-3242\3, 2499-3243\3, > 3244-4057\3, 4061-4979\3 > charset p2 = 963-1650\3, 1653-2496\3 > charset p3 = 1651-2494\3, 3245-4058\3, 3246-4059\3, 4060-4978\3, > 4062-4980\3 > > and TreeFinder files set partitions in a line at the top of the file, like > > "partition" 1112331221111111 > > "taxon1" AACGATTTCTCT > "taxon2" AACGATCTTAT > > Has anybody used an R script for transforming NEXUS SETs into the > treefinder partition? > > Thanks, > > ~John > > > John S. S. Denton > Ph.D. Candidate > Department of Ichthyology and Richard Gilder Graduate School > American Museum of Natural History > www.johnssdenton.com > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Rob Lanfear Research Fellow, Ecology, Evolution, and Genetics, Research School of Biology, Australian National University phone: +61 (0)2 6125 3611 www.robertlanfear.com [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
