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I have used Neighbor-joining to infer a phylogenetic tree. I have also done bootstrapping but it is not clear how to compare the topologies of the bootstrap replicates with that of the original tree. For example, is Node A of the original tree recovered in the Boostrap replicate? What is the algorithm to compare the topology of two unrooted trees?

Example:

Two trees that need to be compared to see if some nodes are different

Tree to be compared to

keterpstra_mwu
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1 Answers1

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Best explanation is given here,

  1. Refer GeeksForGeeks Here
  2. CrazyForCode
  3. StackOverFlow
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dahiya_boy
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  • I need to compare trees are similar or different due to the parent node. The leaf and interior branches would often have different lengths and still be consider a like part of the trees. I guess were are ultimately searching for a similar tree path when comparing trees. I don't know an easy test to do this. The only easy part is matching the trees leaves. I hope the examples trees provide an explanation. – keterpstra_mwu Dec 21 '16 at 02:53
  • I need to compare trees to find if the tree nodes match. As you go toward the root the trees wil have fewer matches. With a very high number of matches as you get toward the leaves. We are comparing the subtrees or nodes to see if they match. I was using the exact match method but this does not cover all the branches that would match. I'll try to put a good example in the question. The blue or aqua text holds two tree diagrams for you to see. – keterpstra_mwu Jan 05 '17 at 03:04
  • Could you explain data or value might be? I'm comparing trees topology which are often similar but have different branch lengths. The bootstrapping matches nodes of the tree with another tree. There are circumstances where the trees appear to be but are actually the same. – keterpstra_mwu Jan 10 '17 at 23:24
  • The last sentence should read: There are circumstances where the trees appear to be different but are actually the same. This is caused by inserting a root at a clade or node near where you are trying to compare.. – keterpstra_mwu Jan 11 '17 at 21:20
  • Could you you please explain what the values are in each node. Are they for instance the length of line on the tree? – keterpstra_mwu Jan 21 '17 at 07:21