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!
Link: http://www.nature.com/nature/journal/v478/n7369/fig_tab/nature10464_F1.html [PAPER][1]
•
written
by
cacaucenturion •
"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"?
Thanks you very much!
"Collapsed" means a group of branches are not shown, usually to make overall tree more visually clear.
Thanks a lot. I got it!
Hi, does anyone have any idea? I am waiting for any reply online.
Log in to answer this question.
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.