read.iqtree and regular bootstrap

[Léo-Paul Dagallier]

Hi,

Let's take the case were a tree has been inferred with IQTREE, but branch support was assessed with non-paramteric bootstrap (BS) and not with UFBoot or SH-alrt.
I just wanted to notify that the read.iqtree() function will correctly read the phylo object of the treedata, but will not correctly read the data. It will in fact consider the BS values as both UFBoot and SH-alrt values.
As there is no way for read.iqtree() to know what type of branch support is in the treedata, I would suggest to add a note on the help of the function mentioning that read.iqtree() has to be used only when UFBoot AND SH-arlt (or UFBoot alone) was used to assess branch support. For BS or SH-arlt alone, users should use read.tree() function instead.

Thanks