Bugs in ancestral output order

[lamthuy]

There is a small bug where the order of the branches:

• in the ancestral output branch 0,1,2

  Seq-Gen/source/evolve.c

  Line 569 in e8660d7

   if (!tree->rooted) 

• while in the WriteTree the order was 1,2,0

  Seq-Gen/source/treefile.c

  Line 567 in e8660d7

   } else { 

This causes issue in parsing the ancestral output.

[Andrew Rambaut]

Thanks for noticing this. I propose fixing this by changing the ancestral output to follow the order given by the tree (1,2,0) as this is less likely to break other things.