Clonalframe To Dnd Conversion

Question

[Lee Katz]

Hi all, does anyone have a script to convert ClonalFrame output to a tree output? I think that it's easy to chop off the first line and grab the tree. However, the names of each node are just sequential numbers and need to be changed back to the original strain names.

I don't think I see a solution in the manual, and unfortunately the GUI is not working on my computer.

http://www.xavierdidelot.xtreemhost.com/files/clonalframe-userguide.pdf

Thanks!

Answer 1

[Joseph Hughes]

You can do this in ClonalFrame, read section 6.3 of the user manual http://www.stats.ox.ac.uk/~didelot/files/clonalframe-userguide.pdf

Alternatively, create a nexus tree file with a translate block. #nexus

begin trees;
  translate
  1 CloneA,
  2 CloneB,
  3 CloneC,
  4 CloneD,
  5 CloneE
  ;
  tree one = [&U] (1,2,(3,(4,5));
end;