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

The size of the points in each plot correspond to the abundance of the clade relative to the entire OTU table and the position on the y-axis corresponds to phylogenetic novelty (mean of summed branch lengths from each terminal node to the closest reference sequence).

Alignments (.afa) and Clades (.tre)

An alignment and subtree corresponding to each ranked clade is output to the results directory. These can be evaluated independently (e.g., [SeaView] (http://doua.prabi.fr/software/seaview), FigTree (http://tree.bio.ed.ac.uk/software/figtree/)).

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