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!
"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.