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 - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
