Phylogenetic placement of NA reads

Continuing my attempts to place these short reads in an evolutionary context, I’ve decided to use all the ‘NA’ OCTUs (which still had no match after the Enoplid DB was added in) from both the A and B datasets clustered at 99%.

Jess had been using the ARB PT server and SILVA reference (non-redundant) database, so that’s what I’ve decided to try and use for aligning my reads (vs. the SINA webaligner and its crappy 300 sequences at a time).  The whole SILVA NR REF database was used to build the User 1 PT server

The ARB database containing the Eukarya Reference alignment only is called SSU_102_SILVA_Eukarya2.arb ; All Reference alignment sequences have been tagged with EukaryaREF in the import field.


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