I am wondering if anyone knows of a phylogenetic software that will allow me to compare the support for a specific partition of species.
More specifically, I am interested in the phylogenetic position of a specific clade X. I want to test whether X is monophyletic with another clade A, monophyletic with another clade B, or whether it is an outgroup to both clades. I want to use a phylogenetic software on some input gene alignment to directly compare how well supported are the different placements of my clade X.
From what I've seen, various phylogenetic softwares like PhyML and MrBayes, show branch support only for partitions in the consensus tree. Is there is some software that will allow me to test the support for a partition of my choosing?