I've been obtaining the location new tips by specifying the edge on the old tree that becomes split upon addition. This has been surprisingly difficult, as all tips and nodes become re-named when new tips are added to the fixed tree, but the tip labels become a fair point of comparison between both original and updated trees.
The pplacer software gives a list of "Edge Numbers" which I believe are the edges on the old tree that our new tips land on, but when I've tried to mannually find these edges (ie. By referencing tip / node labels) my edge numbers do not match up to theirs. I'm pretty certain my manual method is correct (albeit slow) and I'm assuming edge number is reffering to the row in the "edge" table that comes with a phylo object. Are there multiple definitions of edge number? Does it not just mean which(rows(tree$edge)) = edge.of.interest? I've been having trouble clearing it up online, currently going forward with the more complicated manual-find method, but it'd be nice to get them the easy way because pplacer outputs an otherwise pleasant .csv.
ConnorChato
commented
4 years ago
I've been obtaining the location new tips by specifying the edge on the old tree that becomes split upon addition. This has been surprisingly difficult, as all tips and nodes become re-named when new tips are added to the fixed tree, but the tip labels become a fair point of comparison between both original and updated trees.
The pplacer software gives a list of "Edge Numbers" which I believe are the edges on the old tree that our new tips land on, but when I've tried to mannually find these edges (ie. By referencing tip / node labels) my edge numbers do not match up to theirs. I'm pretty certain my manual method is correct (albeit slow) and I'm assuming edge number is reffering to the row in the "edge" table that comes with a phylo object. Are there multiple definitions of edge number? Does it not just mean which(rows(tree$edge)) = edge.of.interest? I've been having trouble clearing it up online, currently going forward with the more complicated manual-find method, but it'd be nice to get them the easy way because pplacer outputs an otherwise pleasant .csv.