Hi Martin and list members, Happy New Year. I'm trying to explore the phylogenetic tree space represented by a few thousands trees of ~2500 tips.
The packages TreeTools and TreeDist, which hold the most advanced R functionality for such analysis (AFAIK) are limited to dealing with trees smaller than 500 tips, presumably due to memory requirements. So my first questions is: what could I do to bypass this limitation? Second, are there alternative packages for robust quantification of phylogenetic space (i.e. not Robinson-Foulds, see Smith 2022: https://academic.oup.com/sysbio/article/71/5/1255/6486431)? My fallback plan is either (1) to trim the trees to genus level and make do from there, or (2) split the trees taxonomically and somehow tally up the results from each sub-tree. Perhaps even better would be to do (2) and then prune out clades that show little between-tree variability before doing (1). Any comments on this plan are more than welcome. My current reviewers didn't respond well to "was not feasible due to computational limitations"... Many thanks in advance for any help or advice! Very best wishes for the new year, Roi [[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/
