I'm playing around with sequences I have from amplifying nematodes from fecal samples. What I'm ultimately trying to do, would be identifying nematode-species by their 18S sequences. Now I'm looking for good software to deal with my data. Blast+MEGAN works just fine and it seems my sequences are good, but I'd like to group them to the OTUs - Megan leaves quite a many of them to the level of Nematoda and I'd like to find out if they would be clustering to multiple OTUs.
I've tried PANGEA but apparently that's good only for prokaryotes and RDP (at least I can't modify taxcollector-database from NCBI databases). So, are there any softwares which could be used to pipeline all my samples or do I have to use separate programs to denoise, cluster and identify?