Tips for custom tree scaling

[A O]

Hello,

I have seen a few methods for inserting a scale under a phylogenetic tree, and/or using branch scaling based on information in the tree file (ex. branch lengths in newick files), or from data files that are outputs from other phylogenetic software.

I have manually created a phylogentic tree in newick format of a small number of species (~20) and can read it and display it without issues in ggtree. I would like to manually scale the branches of the tree to reflect divergence times of the species of interest using dates from the literature. These dates are on the scale from tens- to hundreds-of-millions of years. The ggtree manual suggests the R package "deeptime" for displaying trees on geological timescales. However, it seems that deeptime and also methods using ggtree require files containing the information given from various analyses. In other words, the scaling information of branches comes from other analyses.

What would be the best method of using my "own" (literature-derived) dates for scaling tree branches, and to display a geological timescale underneath? I have tried manually adding my own branch lengths directly in the newick file with limited success. For instance, I tried using raw values, and also by normalizing each branch length value to the oldest divergence time. However, things get tricky when it comes to the display, and maniupulating the newick file by hand is extremely cumbersome.

It seems I need a method of converting millions of years in divergence times to a ratio that can be used as branch lengths in the newick file. Does anyone have a suggestion?

Thanks in advance,

A