Time Tree using ape:: chronos

[walkyshitake]

Hello,

I was noted on the recent post regarding the time tree input for CAFE5. As my previous workflow was to use OrthoFinder's make_ultrametric.py, I am currently doing a re-run using the recommended ape::chronos function for the time tree construction.

As I am still learning how to properly use the package, I wonder if you could kindly provide a demonstration or example workflow for chronos. it would be extremely helpful for understanding the preferred practice for a valid input for CAFE5 analyses.

Thank you very much for your time and help.

D

[benfulton]

Here is an R file that replaces the r8s call in the tutorial example. In the tutorial, you would run

python prep_r8s.py -i maximum_likelihood_tree.txt -o r8s_ctl_file.txt -s 35157236 -p 'human,cat' -c '94'
r8s -b -f r8s_ctl_file.txt > r8s_tmp.txt
tail -n 1 r8s_tmp.txt | cut -c 16- > mammals_tree.txt

You can replace this with

Rscript chronos_time_tree.R maximum_likelihood_tree.txt mammals_tree.txt human cat 94

Let me know if you have any questions.

chronos_time_tree.zip