Hi @Adrian_08, it sounds like maybe you didn't run all of the commands that @gregcaporaso suggested in your QIIME 2 conda environment. You need to make sure that your conda environment is activated first - if you followed our docs, that environment would be named qiime2-2017.4, so, you would run something like this:
source activate qiime2-2017.4
conda install -c bioconda fasttree
conda install -c qiime2 q2-phylogeny
Hope that helps!