The Tree Viewer
About The Tree Viewer
About
Collection and population core-based trees are displayed using the PhyloCanvas software, also from the CGPS. The PhyloConavas software is under active development, and we expect to bring new features regularly to Pathogenwatch - so apologies if some of the description below is no longer up-to-date. The displayed trees are fully interactive and allow the drawing of subtrees, selection of assemblies by clicking on parent nodes, and highlighting the phylogenetic distribution of AMR and other metadata.
Selecting Assemblies
Assemblies can be selected by either clicking on specific leaves or by clicking internal nodes, and are highlighted with a purple halo. Selected assemblies are highlighted in the Map View also with a purple halo and shown exclusively in the Metadata Tables.
Manipulating the tree
The tree can be moved and zoomed in or out using the touchpad (two fingers to zoom) or mouse (middle wheel).
Further controls can be accessed by clicking the toggle switches on the top right. These give you access to the layout algorithm, node size, label size and data export functions (such as Newick file of the tree for download).
Right (mouse) or two fingers (touchpad) clicking on an internal node brings up further options. Of particular use is the "Redraw Subtree" function, which will redraw the tree with just the assemblies in that clade.
With very large trees - thousands of assemblies - using the "Redraw Subtree" function to examine clusters of interest will speed up the performance of the site. Combined with the History feature, you can still quickly move between different subsets of the assemblies.
Tree History Panel
The tree history panel stores a small image of each version of the tree that you generate, including changes in layout or after using "Redraw Subtree". Clicking on the image will return the tree to that layout. The history is only stored for your current session and not preserved after closing the browser window.
Population Trees
About
The default tree shown is built from the assemblies selected for the collection. For species where sufficient high quality assemblies are available, Pathogenwatch provides a way to view collection assemblies compared to public subsets of the wider population.
A toggle in the top-left allows you to switch to the "Population Trees". Clicking "Population" will first bring up a tree of the references used to represent the species distribution.
Reference Subtrees
Leaves of the population tree that contain assemblies in the collection are highlighted in purple. The name of the reference assembly is given, followed by the number of assemblies from the collection in that cluster, and finally in square brackets the number of public genomes in that cluster.
Clicking on a highlighted reference will then draw a tree for the reference cluster, containing both the collection assemblies and the public set.
These assemblies are also displayed in the Map View and Metadata Tables, and can be filtered and queried as normal.
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