SILVA Tree Viewer User Guide
The Tree Viewer is a web application designed to allow users browsing large phylogenetic trees (larger than 2 Million nodes) without requiring the download of specific software tools or data files. The viewer currently provides direct access to the phylogenetic trees provided with each release of the SILVA rRNA database. Search and browsing functions are provided to allow users quickly finding their data of interest. The viewer provides only visualization tools and no editing of the trees is supported by the current version (1.1).
The Tree Viewer interface consists of the following main elements:
- main display, which is the area of your browser containing the Tree Viewer (or your whole screen in full-screen mode)
- tree area, which consists of the background where the elements of a phylogenetic tree are shown
- controls buttons, found along the upper portion of the left border of the main display
- scrollbar, located in the bottom portion of the left border of the main display, which provides an overview of the current displayed tree portion with respect to the full tree
- taxon bar, located at the bottom of the main display, providing details of an on screen taxon
- taxonomy brackets, appearing over the right portion of tree area, which show taxonomic information for the displayed portion of the tree
- feedback button, located in the middle of the right border of the main display, it gives access to the feedback system, where support requests (including reports about taxonomic data) can be filed
- scale, providing a reference for interpretation of the (horizontal) branch length at the current zoom level
Moreover, other elements are shown according to function being used or following interaction with the main controls. Such elements are called panels and windows. Panels appear sliding in/out either at the right or left borders, over the main display. Windows appear normally in the middle of the main display, requiring the user to complete an interaction before they can be dismissed. Those elements are described later on in the related function sections
Finally, the interface provides a full-screen mode that can be activated/deactivated with the full-screen control button (rectangle corners icon).
Navigation (Tree area pan and zoom)
The phylogenetic tree is shown on the background, under any other interface element and has the following main characteristics:
- The tree is always "exploded", meaning that no folding of groups is supported. To compensate for that, the groups are shown as colored polygons, enclosing all sequences belonging to them and the viewport is organized into zoom levels, allowing to get an overview of a tree section (lower zoom levels) and zooming in to any area of interest (higher zoom levels)
- clicking on a taxon polygon zooms the current tree area to the extent of that taxon
- The tree can navigated according to the following interactions
- panning, the view can be panned with the mouse (holding left mouse button) or with the arrow keys
- zooming, the zoom level can be changed using the mouse wheel, the + and - keys or the + and - control buttons (the third button shows the current zoom level and is not clickable)
- Sequences are located at the end of the branch leading to them and have no special marker unless they are selected / highlighted.
- Sequences are labeled: clicking on a sequence label brings up the sequence details panel on the right side of the main display. This panel provides details about the sequence directly from the SILVA website, if available.
- A scrollbar shows your viewport of the whole tree: since large phylogenetic trees can get very long along the vertical axis, the scrollbar on the left of the main view gives a feeling about where the currently displayed portion of the tree lies, with respect to the entire tree. The scrollbar represents the complete vertical extent of the tree, independent of the current zoom level. A blue marker on it shows the position of the current tree area. If the displayed tree portion is too thin to be shown (higher zoom levels) an horizontal line shows its approximate location.
Taxonomic context information
Taxonomic context information about the currently displayed tree portion is provided in two ways: Taxon bar and taxon brackets. The taxon bar is shown in the bottom part of the main display and shows information about the Taxon currently laying under the mouse pointer. Information is given in the following format:
- Current taxon: Full_taxon_path ( taxon_rank sequences_count polyphylogeny_information )
Taxonomy Brackets are shown on the right portion of the tree area and consists of vertical square brackets according to the vertical extension of taxonomic groups "crossing" the current view of the tree. The brackets are shown from right to left according to their rank (Domain is the rightmost). The amount of brackets shown is dynamically computed to ensure high performance in visualization, hence at lower zoom levels only few ranks may be shown, whereas the full path can be shown at higher zoom levels for the groups of interest. The taxonomy brackets overlay can be toggled clicking on the taxonomy brackets button (property window icon).
The Tree Viewer provides search functionality via the search panel, which can be accessed by clicking the search control button (magnifying glass icon). The search panel provides rapid search and browse functionality to allow the user locating data of interest in the tree.
Search for sequences
There are two possible ways to search for sequences according to their metadata
- By accession number, which returns any sequence whose accession number starts with the given text. The search includes start and stop positions, separated by full stops (i.e. the complete accession is taken to be Accession_number.start.stop
- By full name, which returns all sequences whose name contains the given text.
This search type returns sequences as circle shaped features which are loaded to the Results navigator for browsing by the user
Search for taxa
There are two possible ways to search for taxonomic groups
- By taxon name, which returns taxa whose name contains the given text
- By taxonomic path, which returns taxa having the given text as part of their full taxonomic path
- Note that since all taxa within a lower rank taxa will match the search condition, only the lowest (more generic) rank result will be returned
This search type returns taxonomic groups as rectangular features which are loaded to the Results navigator for browsing by the user
Browse Phyla (Phyla browser)
The phyla browser can be found in the search panel where Phyla (Kingdom/major clades for Eukaryota) are listed as clickable elements. A click on the phyla name loads all taxonomic groups comprising it (more than one in case of poly-phylogeny) to the viewer and zooms the view to the first result. The Results navigator is also shown, allowing to navigate the loaded groups.
The Results navigator is automatically shown in the top right corner of the viewer when a set of results are returned from a search operation. The results can be navigated through by clicking on the navigator buttons. It allows forward and backward browsing, provides the index of the current feature along with the number of total features loaded. Show all tries to fit all results on the tree area (note that if results are far apart it might not be possible to see them all even at the lowest zoom level)
Navigation can be ended with "End Navigation", thus closing the navigator and removing any highlight of features from the viewer.
Clicking on the feedback control brings up the feedback system which consists of a set of windows driving the user interaction. First of all a choice is presented to the user among the different type of feedback that can be given
- Report a data problem, can be used to report wrong classification of a sequence, errors in the taxonomy and any other problem with the phylogenetic data. Reporting a data problem is a two step process
- First the data affected by the problem to be reported has to be selected (picked), this can be done by clicking "Pick data", which puts the viewer in pick mode. The user can then click on sequence labels and on taxonomy groups (colored rectangles) to toggle their picked status. Clicking on "Clear selection" removes all picked item from the current selection, while clicking on "Done picking data" brings the user back to the feedback system, where a list of selected items is provided: on that screen, clicking on "Proceed" will now bring the user to the second step
- The data problem report form is automatically filled with the selected data; the user has then only to provide a description of the problem and contact information
- Report a technical problem, used to report technical issues (bugs) in the Tree Viewer itself
- Propose an improvement, used to propose any kind of improvement for the tree viewer, including new interactions with the tree
- Other feedback, used to ask questions or give any feedback not fitting in the former categories
The settings panel can be opened by clicking on the settings control button (cog shaped icon), the panel is divided into sections, each enabling a specific customization as described below
Node Display Setup - Sequence Label configuration
Each sequence in the tree will be labeled according to the fields checked in this section. The following fields are available
- Accession (acc.start.stop)
- Full Name
- Isolation source
- Sequence quality
- Alignment score
SILVA Treetype selector
The tree viewer currently supports two SILVA guide trees
- SSU Ref NR 99 : This fully classified, manually curated tree is included in the recommended reference database. The database is based on the Ref dataset with a 99% criterion applied to remove redundant sequences using the UCLUST tool. Sequences from cultivated species have been preserved independent from prior filtering. It can be used as a representative dataset for phylogenetic analysis and classification.
- LSU Ref : This fully classified guide tree is included in the LSU reference database containing only high quality, aligned 23S/28S ribosomal RNA sequences with a minimum length of 1900 bases.