Dear all, I am trying to make a phylogenetic tree with pie charts showing a relative frequencies of the three quartet topologies around a branch in the ASTRAL species tree (similar to the Fig. 7 in Sayyari & Mirarab, Molecular Biology and Evolution, 33: 1654-1668; https://doi.org/10.1093/molbev/msw079). I am computing the species tree in ASTRAL with option '-t 8' or '-t 4'. This produces a tree with frequencies of alternative quartet topologies saved as bootstrap support values, e.g.
((species1,(species2,species3)'[pp1=0.75;pp2=0.24;pp3=0.01]':1.2003685744180 805)'[pp1=0.98;pp2=0.02;pp3=0]':0.9679599282730038,((species4,species5)'[pp1 =0.88;pp2=0.11;pp3=0.01]':1.2454851536484994)) However, I am unable to load such a tree into R using standard functions as 'read.tree' or 'read.newick'. I have two question: 1. Do you know how to read this tree into R? 2. Could you suggest any trick how to use these values (e.g. pp1=0.75;pp2=0.24;pp3=0.01) to draw pie charts over nodes/branches? Thank you. Tomas Fer Department of Botany Prague, Czech Republic _______________________________________________ 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/
