I am reading on the topic of phylogenetics/phylogenomics in the presence of gene flow for my PhD in plant phylogeny and it seems that there is no method specifically aimed at building phylogenies when gene flow/introgression/hybridisation is suspected.
Instead, people separately build the phylogeny and then use various methods to detect introgression, e.g.: Wang et al., 2020 (https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.16215).
But this might bias results by using an incorrect phylogeny over which to overlay hypotheses for introgression events. Does anyone know of methods where gene flow is explicitly taken into account for phylogeny building?