You could do a bayes factor test using MrBayes or BEAST, by applying topological constraints. This is an elegant solution for conducting explicit topological hypothesis tests. But you aren’t likely to get BEAST or MrBayes to run with 200kb. I’ve been thinking about doing this myself with data partitions generated from partition finder (For example).
I think I once tried loading 500kb into MrBayes and it gave me some kind of warning that it can’t read alignments longer than ~90kb. Talk about a 21st century problem. Jake > On Apr 19, 2016, at 7:06 AM, Chris Buddenhagen <cbuddenha...@gmail.com> wrote: > > Dear all > > What is the best (statistically defensible) way to test different > hypotheses regarding topology? I have data from hundreds of > loci....concatenated alignment is approximately 200 kilobases. > > For example one taxonomist divided the tribe of plants I am working on into > two main groups (presumably sister to each other). Also one genus is > apparently embedded in the other, and was treated as separate. Another > division in the taxonomic treatment identifies major groups above sections. > > Sincerely > > > Chris Buddenhagen > cbuddenha...@gmail.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/ _______________________________________________ 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/
