The emissions are a little better. Essentially, you're going to end up with a synthetic diesel. It's a fatty acid methyl ester, FAME. Simple transesterification gets you biodiesel, but it's a second- or third-generation biodiesel, depending on how you look at it. Oil is squeezed out of the algae as any soy oil would be squeezed out of soy.
The remaining biomass can be used as a relatively mid-grade coal, around 9,000 BTUs per pound, but the emissions profile in both cases is better than the emissions profile you would typically find in a similar fossil-derived diesel, because there is less sulphur in it.