This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Clonalframe To Dnd Conversion

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!

phylogeny
• 2,805 views • link
updated by Biostar Biostar • written by Lee Katz Lee Katz

1 answer

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;
• 0 views • link
written by Joseph Hughes Joseph Hughes

Log in to answer this question.

More posts like this