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).

Interface overview

The Tree Viewer interface consists of the following main elements:

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).

OVERVIEW PICTURE

Features

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:

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:

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).

TAXONOMY BRACKETS

Search

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 PANEL

Search for sequences

There are two possible ways to search for sequences according to their metadata

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

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.

Results navigator

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)

RESULTS NAVIGATOR

Navigation can be ended with "End Navigation", thus closing the navigator and removing any highlight of features from the viewer.

Send feedback

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

FEEDBACK SYSTEM OVERVIEW

Customize settings

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

SETTINGS PANEL

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

SILVA Treetype selector

The tree viewer currently supports two SILVA guide trees