How to keep only one sequence per species (after the remonal of the outliers)?

[yannisdim]

I use ReproPhylo and metaBEAT to download sequences for specific genes for a list of species. The only problem I have is that I end up with multiple sequences per species, which leads to trees with clades with multiple terminal nodes for a single species. Because this is a problem for the analysis I want to do later, is it possible through ReproPhylo (or metaBEAT) to keep only one sequence per species? Many thanks in advance!