Phylo Explorer

"Phylo Explorer" is an interactive visualization tool,
that allow the users to browse the phylomes
in our database and have a better view of the relations
between the species and the phylomes they are in.

Selecting the species to be included in the explorer:
Searching and selecting by taxonomy names or taxonomy identifiers,
species can be explicitly included in the generation of the explorer.

*Only phylomes which contain all the selected species will be included.

Description of the explorer's components:
Each column represents a phylome and each row a species.
The color of a cell in the cross section indicates if the phylome of that column in
what percentage contains that species in all of its trees.

• The dendrogram on the left side of the heatmap represents a taxonomy tree of the included species,
  corresponding to the relationship of their lineages.
• Columns are labeled with the identifiers of the included phylomes.
• Rows are labeled with the taxonomy names of the included species.

Meaning of the colors in the heatmap:

• Each shade of the green color increments by each 10th percentage value of the species presence in all the phylome's trees.
• Grey means that the phylome does not contain the species.
• Black means that the species is present in all of the phylome's trees.
• Red means that the species is the seed of the phylome.

Narrowing down the explorer to certain species:
To reduce the explorer's content for a specific combination of species after the first inclusion,
the filter bar can be used (first search bar directly above the dendrogram) to search between the included species and select them.
After the selection, to initialize the filtering, click on the "Filter" button.

Selecting the species of interest to search:
By clicking on the cells or the dendrogram labels, species can be selected to get a data table of those phylomes,
which include the combination of the selected species in all their trees.

*Once the species are marked, click on the "Get phylome table" button.

Checking out phylomes:
PhylomeDB has the option to browse phylomes as a data table ("Search" -> "Phylomes"),
but a phylome's content can be accessed by clicking on the explorer's column labels.