Step 3. Interpreting results

Within the results directory there are a series of files, including plots visualizing the phylogenetic novelty within your study, alignments and trees for each novel clade ranked by abundance and novelty, and HMMs representing each alignment that can be used in downstream analyses.

Plots

Alignments (.afa) and Clades (.tre)

Alignment HMMs

Each novel alignment is used by hmmer to build a nucleotide HMM that can be used to query a different data source for a genomic or metagenomic context for the novel clade (i.e., identifying contigs in an assembled metagenome that correspond to the novel clade identified by SSUnique).

To run such a search using nhmmer:

nhmmer -o novel_clade_nhmmer.output novel_clade_model.hmm contigs.fa