How to Installing & Using RDP Classifier through bioconda?
The benefit of using the conda package is that you no longer need to know or care exactly where the jar files are (that many java-based packages require this is TERRIBLE design). The example java -jar ... command in your post becomes:

Clustering derep -m '#=GC_RF' -o derep.fa all_seqs.ids all_seqs.samples alignment/*.fasta


in the bioconda version. In bioconda packages, there are wrapper (usually python) scripts meant to provide somewhat friendlier interfaces to java programs that otherwise lack executables. In this case, RDP Classfier has the following executables in bioconda:


AbundanceStats
AlignmentTools
Clustering
FrameBot
KmerFilter
ProbeMatch
ReadSeq
SeqFilters
SequenceMatch
hmmgs
classifier


If you really want to know, the .jar file is under $PREFIX/share/rdptools-$PKG_VERSION-$PKG_BUILDNUM/, where $PREFIX is where ever the environment is and the other two variables indicate the package version and build number (at the moment, rdptools-2.0.2-1 would be the likely folder name).