difference between subtrees and clones?

[aelhossiny]

What is the difference between the clones and the subtrees? It seems that both are pseudobulk representation for the phylogeny analysis but I am not sure what is the difference between both.

Thanks

[teng-gao]

Hi @aelhossiny ,

In a phylogeny with mutations placed on the branches, the subtrees are the clades, whereas clones are groups of cells that have the same set of mutations (could be monophyletic or paraphylytic). In the example tree below, each star marks a mutation on the tree. There are 3 subtrees (clades) defined by each of the three mutations (blue, red, blue+green). Green by itself is not a subtree because it's not a clade. The mutations also define 3 clones, which are blue, red, and green.

[aelhossiny]

That's helpful! Thank you!