Multiple gene trees outputted

[ksiewert]

Hello,
When I use the -T option to output the gene trees, along with a recombination value above 0, more than 1 gene tree is outputted for each replication. Do each of these trees represent a chunk of the genome that has not experienced recombination? What is the meaning of the order of these trees? For example, is there one that we know is the tree corresponding to the selected site?

Thank you!