VAMPS-Taxonomy Navigation Help

1. There are 6 taxonomic ranks in this software
   1. The taxonomy is based on the RDP Taxonomic Classifier
   2. The ranks are:
      1. Superkingdom
      2. Phylum
      3. Class
      4. Order (often seen as 'orderx' due to conflicts with the MySQL 'order by')
      5. Family
      6. Genus

2. 'NA' means there is no data for this taxonomic rank.
   1. These 'NA's are caused by either:
      1. 'no_blast_hit'
      2. 'no_consensus_taxonomy'
      3. 'no_ref_taxonomy'
   2. showing up in the 'Superkingdom' rank

3. Taxonomic groupings
   1. They will show up in your pie charts
   2. They are used to compute Bray-Curtis distances for the heatmap.

4. There are two checkboxes that you can use to choose your taxonomic groups.
   1. The checkbox to the left of the File Folder Icon
      1. If you check this checkbox , You will choose everything at the next lower taxonomic rank.
      2. Thus , if you choose the leftmost checkbox for 'Archaea', you will actually be choosing :
         1. Crenarchaeota
         2. Euryarchaeota
         3. 'NA'.
      3. Data will be grouped at those taxonomies.
   2. The checkbox to the right of the File Folder Icon
      1. If you check this checkbox, You will choose only that taxonomy
      2. Data will be grouped to that taxonomy.