possible issue with species overlap threshold

[rderelle]

there might be a problem with the way the species overlap threshold is implemented.
With default parameters, sos_thr = 0, ete3 reports speciation events in my tree. However, when increasing this threshold, even marginally (e.g. sos_thr = 0.0000001), no speciation event is reported while we would expect to have more (or at least the same number).

If correct, I think the problem comes from here:
https://github.com/etetoolkit/ete/blob/master/ete3/phylo/spoverlap.py

    # If species overlap: duplication
    if score > sos_thr:# and d > 0.0: Removed branch control.
        event.node = current.up
        event.etype = "D"
        event.outparalogs = set([n.name for n in sister_leaves  if n.species == ref_spcs])
        event.orthologs   = set([])
        current.up.add_feature("evoltype","D")
        all_events.append(event)

    # If NO species overlap: speciation
    **elif score == sos_thr:**
        event.node = current.up
        event.etype = "S"
        event.orthologs = set([n.name for n in sister_leaves if n.species != ref_spcs])
        event.outparalogs = set([])
        current.up.add_feature("evoltype","S")
        all_events.append(event)
    else:
        pass # do not add event if distances == 0

I do not quite understand the 'elif score == sos_thr:' ... there should be cases where score < sos_thr (e.g. cases where speciation events appear because the score is below the threshold).

best,
Romain

[jhcepas]

Hi Romain,
I think you are right. This code comes from early ETE times (2007), and to be honest we never use sos_thr != 0. I will fix it asap

[jhcepas]

I also noted that this was only affecting to 'get_my_evol_events' but not 'get_descendant_evol_events'

[rderelle]

Hi Jaime (hope you are doing great),

I haven't used the 'get_descendant_evol_events' function.
At the end, I wrote my own function that is slightly different from the 'get_my_evol_events'. But I wanted to point the issue in case other peoples were interested in using 'get_my_evol_events'.

cheers