Hi, I am running phylonet to estimate network with ILS + gene flow. I am doing Maximum Pseudo-likelihood (network_MPL).

However Iam not sure if my input gene trees can/must be ultrametric (without branch lenght). In one of the paper of the authors they said branch lenghts are not allowed (Inferring Phylogenetic Networks Using PhyloNet, Systbiol 2018).

But the input files for MPL gave as example on the website of the software have branch lengths. Is someone know waht is correct?

thanks