Closed Tonny-zhou closed 2 years ago
If you have an outgroup in your tree you could first use it to root the tree (using ape::root
) then remove the outgroup (using ape::drop.tip
) and then run the BactDating analysis on the remaining tree with root known (using bactdate(...,updateRoot=F)
If you have an outgroup in your tree you could first use it to root the tree (using
ape::root
) then remove the outgroup (usingape::drop.tip
) and then run the BactDating analysis on the remaining tree with root known (usingbactdate(...,updateRoot=F)
Dear author,
I followed the above actions, however, the results of roottotip function seemed wrong, as the warning message said "The linear regression suggests a negative rate". However, if i used the result of initRoot function as the input tree for roottotip function, the results seemed reasonable. So, does it mean the outgroup within my tree is not suitable? but i used the outgroup from the publication reference. I really hope you could solve my doubts.
Yours, Tonny
Yes, it seems that the outgroup is giving a false impression for the location of the root in this case, which can happen especially if the outgroup is very distantly related.
Dear author,
Thank you for this great dating tool! I have a small question, i.e., is it possibile for user to specify the name of the outgroup within the input unrooted tree? I know the input tree for main function bactdate is a unrooted tree, so I guess whether supplying the outgroup could help to detect the best root position?
Yours, Tonny