Brad Jones

I would note that with @GuangchuangYu's solution, the breaks need to specified in terms of the amount of time since the root of the tree. This is because with the...

The conflict appears to be with `tidyverse` not `ggtree` as the following code gives the same error: ```r library("tidyverse") library("RNeXML") f

You can use the package, `ape`, to root the tree with respect to an outgroup. ```R library(ape) library(ggtree) tree

If you want more control of over the contours you can adjust the x scale (from @GuangchuangYu's example) : ```R ggtree(x) + theme(panel.grid.major=element_line()) + layout_circular() + scale_x_continuous(breaks=c(1, 2, 3)) ```...

A proper minimal example would help people to better help you fix your problem. For example, it would help to `dput()`, `MSA.alnFasta` and `SampleTree`.

You can use the `reroot` function in phytools to get better control of the rooted tree's branch lengths. To outgroup by the 4th tip: ```R library(phytools) library(ape) set.seed(1) tree

This is a bug in the package, ape (`read.tree` / `read.newick` use ape to read the tree). It is fixed in the development version of ape. Install that version via:...

It now works in my fork. See #222 . Though I think this functionality should be available in ggtree proper at some point.

I have built a workaround for this in 5a70208dbea02567bd11eec7fe2e99ef369b3ef9. `ggdensitree` will set the maximum tip date to 0 when `align.tips = TRUE` (the default). So, ```R trees

I'm not super familiar with dendroscope, but it's possible that dendroscrope does not display the tree scaled by edge length. If there are really short edges in your tree they...