There are lots of teams doing Astrobiology in Europe, but unlike in the US, they are not grouped under a name, as in the case of NAI. There are centres for astrobiology in Madrid and Edinburgh, and the Nordic Network of Astrobiology (all of them associated to NAI). On the other hand, there are teams working in Astrobiology in many universities and research centres across Europe as well as national space centers such as the DLR in Germany. The approach when searching for a doctoral programme is therefore more individual, and you should focus on looking for experts on a specific discipline rather than an astrobiology doctoral program. There is a yearly conference, EANA (European Astrobiology Network Association) where you could find a nice overview of the different research teams and topics. This year there was also the first symposium of Astrobiology graduates in Europe (AbGradE), that will continue on alternate years. Both meetings in 2014 were last month, and unfortunately, I personally didn't meet any person based in Portugal to put you in touch with.
Hope that helped!