Some way to track lineage for each recombination break?

[cizydorczyk]

Hello,

Is there some way to track in which branch of the tree/lineage a given recombination break (given in -b or -f output files) occurs?

I ask because I am specifically interested in identifying simulated recombination events using a tool such as ClonalFrameML, which outputs identified recombinant regions, but the -b and -f options seem to only output START and END locations of the breaks...but not which lineages/leaves they are found in.

Any help is greatly appreciated.

Thank you,
Conrad Izydorczyk

[MonicaDonegan]

Hi Conrad,

Did you find a way to resolve this issue? I am running into the same trouble, and would like to identify which branch of the lineage corresponds to each recombination break.

Thanks,
Monica