search

neherlab / treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
MIT License
224 stars 55 forks source link

Not generating confidence intervals of divergence times, rate or root date #254

Open katie110621 opened 1 year ago

katie110621 commented 1 year ago

Hi! Thank you for this very useful tool!

My output does not contain confidence intervals even when I pass the command --confidence. below is what i am running on the command line:

treetime --tree DEN4_Study_Tree_Aug.nex --dates DEN4_Study_Only_Dates.csv --aln DEN4_All_Aligned_QC_RootSeqRemoved.fasta --relax 1.0 0 --confidence --outdir DEN4_TreeTime_Relaxed_Uncorrelated

Output is here https://www.dropbox.com/scl/fo/vsm70rce6emb2m4eubjrq/h?rlkey=48rw4guzdmljnitd1ypijvd7u&dl=0 and input files are here https://www.dropbox.com/scl/fo/vy0g97nd073ves5x2bosc/h?rlkey=c313vi9jwu0pvtrnyhw8fl7li&dl=0

Unsure what I am doing wrong/if there is something else I need to add to the command line to enable estimation of confidence intervals.

Thank you!!!

rneher commented 1 year ago

This is a poorly documented requirement, but you need to either supply treetime with a standard deviation of your clock estimate (add something like --clock-std-dev 0.0003 to the command) , or run it with --covariation.