Taxonomy browser and understanding genome filters
The taxonomy browser serves the dual purpose of 1) interactively displaying the relationships between various species and 2) intuitively finding and querying multiple genomes of interest. To query a particular set of genomes, it is first necessary to create a genome filter, which simply associates one or more genomes with an arbitrary, user-defined name. After successfully creating a genome filter, it will appear in the scope drop-down box of the search panel. To use a genome filter, simply choose one from the scope drop-down box and perform a search as normal.
The classification level represents the depth or extent to which genomes are grouped taxonomically. The current taxonomy level defaults to 'Major taxonomic group' and is shown in bold with a light gray border. The 'Major taxonomic group' is distinct from the other classes in that it groups all taxonomies at the phyla level, except for proteobacteria, which is conveniently expanded to the class level. To view the taxonomy tree at a different level, simply click on the other classification level links (e.g. Kingdom, Phyla, etc.).
The second alternative method selects/deselects multiple genomes that all belong to a particular taxonomic designation. Clicking on the checkbox beside a taxonomic designation (and not the actual genome) selects (or deselects) all the those genomes belonging to this group. For example, to select all Cyanobacteria, make sure the taxonomy level is set to phyla and then check the checkbox beside Cyanobacteria. Expanding the Cyanobacterial group will reveal that all cyanobacterial species have indeed been selected.