I have a question about the statement "Branches corresponding to partitions that were reproduced in less than 50% of bootstrap replicates are collapsed". In the following paper, the author mentioned it whereas in the tree we can see nodes with bootstrap values lower than 50. I am confused by this. Could anyone lend me a hand? Thanks a lot!
Note that bootstrap values are associated with branches, not nodes. This is an important distinction - if you spend some time reading and thinking about how bootstrapping is used in the context of trees, and the role of bipartitions in this process, hopefully it will become clearer.
"Collapsed" branches refer to those black or grey triangles you see in the figure. A triangle represents a branch, whose internal bootstrap values are lower than 50%. Therefore, drawing them out cannot convince readers. Therefore, the authors chose to hide them in an triangle. This is a common way of displaying trees.
You can try this by yourself: Open your tree in FigTree, select a branch, click "collapse". You will get a triangle.
Thanks! Many branches are collapsed, however there are two nodes with bootstrap value lower than 50 which are not collapsed. I think this is not very rigorous if the authors have mentioned that "Branches corresponding to partitions that were reproduced in less than 50% of bootstrap replicates are collapsed"?
Note that bootstrap values are associated with branches, not nodes. This is an important distinction - if you spend some time reading and thinking about how bootstrapping is used in the context of trees, and the role of bipartitions in this process, hopefully it will become clearer.