Exporting molecular clock outliers using treetrime

1

Hi all,

What is the best way to perform root-to-tip analysis using treetime, and export the molecular clock outliers that are flagged during the process?

I’m trying to use the treetime Python package for that, using a script to export the data processed int he lines below, but I’ve not been able to get treetime to run on python.

    tt.clock_filter(reroot=reroot, n_iqd=clock_filter_iqd, plot=False)
    leaves = [x for x in tt.tree.get_terminals()]
    for n in leaves:
        if n.bad_branch:
            output.write(n.name)

Any suggestions?

2

Hi Anderson,
this should work. what is the problem you are running into?

3

Hi @rneher,

I was getting an error message: raise MissingDataError("ERROR: ALMOST NO VALID DATE CONSTRAINTS")

The TSV file I was using had strain and date columns. Not sure what was wrong, but I guess I need to convert dates from YYYY-MM-DD into numerical format, using get_numerical_dates, like augur refine does. But I’m not sure if that is the solution.

I switched to the standalone treetime installation, and figured out that the output dates.tsv lists all the outlier with their dates as “--”. So, I managed to get the list of molecular clock outliers in that way.

Thank you.