Personal accounts in iTOL

Creating an account in iTOL gives you the possibility to easily organize your trees and have an oveview of their features, datasets and saved views. Trees are grouped into different projects, and these can be arranged into different workspaces. You can add and remove datasets without having to upload your trees again. Saved views are automatically grouped according to the tree they belong to.

Since all the data is stored locally in iTOL, you can access in from anywhere, using any browser.

Projects and workspaces Use projects to organize your trees into categories. You can create unlimited number of projects, and each project can have unlimited number of trees (until our IPO, when we'll have to impose user storage limits :). To help you manage large number of projects, they can be further organized into workspaces. Projects can be collapsed and reorganized on the page by dragging their title bars. Function for moving project to a different workspace is available in the project options pulldown menu. You can change the name or description of projects, workspaces and many other fields by simply clicking on them. Fields which can be edited will be surrounded with dotted lines when mouse pointer is above them. Create new projects and workspaces by clicking on the correponding links.

A personal account in iTOL (click to enlarge)

Moving trees

You can easily change the location of a tree by using its movement controls. The controls are: Up and down buttons: change the position of the tree within its project. Drag button: click the button and drag the tree to another project in the same workspace.

Moving projects

To move a project and all its trees to another workspace, click the Move to workspace link in the project options popup. Select the target workspace from the list, and the project will be transfered there.

Removing items

Most items on your personal page can be deleted by clicking on the correpsonding icon (). Workspaces, projects, trees and saved views can be removed. Note that you cannot remove the current workspace. Mouse over the workspace name, and the close icon will appear :.

You will always get a confirmation dialog before the item is actually deleted. Once item is deleted it cannot be restored. You will have to create/upload it again if you do it by mistake.

Shared projects

You can simply make your iTOL trees available to others. Any project in your workspaces can be marked as 'shared'. Use the "Toggle project sharing" function in the project options popup to change the shared status. Shared projects will have an extra icon in the header () and the project background will be light yellow.

Send your login ID to your colleagues or friends, and they can type it into the box on the SHARED PROJECTS page to see all your shared projects. They will be able to view and export the trees, but not modify or delete them. If you want to share a particular view of a tree, use the 'Save current tree view' box in the top right of any tree display page. These saved views will be available to anyone accessing your shared trees.

Shared projects can also be accessed through a simple URL: http://itol.embl.de/shared/loginID

Each project box shows the name and the description of the project. These can be changed by clicking on them. Below the description is the main table which shows all trees associated with this project. It is described in detail in the following sections. On the bottom of each project box is the link which will take you to the tree upload page for that particular project.

Tree table

The main table in each project shows all relevant data for its trees. Use the move control buttons to change the position of the tree within the projct, or drag it to another project in the same workspace.
Clicking the tree name will display the tree in iTOL. There will be several new features on the display page, which are described below, in the Other features section.

Datasets

All datasets associated with a tree will be shown in the Datasets column. Mouse over any of the dataset boxes to display a popup showing the dataset type and label. You can also remove a dataset or change its color using the functions at the bottom of the dataset popup. Note that you cannot change the color of the 'Color gradient' dataset type, as original data is needed to calculate the color values.

Saved views

If a tree has any associated saved views, a Show link will appear in the Saved views column. Mouse over it to display a popup showing a list of all saved views for that tree. Each saved view's label and note will be displayed, together with a 'delete' button. Clicking on a label will display the tree and resotre that saved view. You can change the saved view's note by clicking on it.

Tree features

The Features column displays various icons, based on the tree features.

These are the possible icons:

Icon	Feature
	Bootstraps: branches have bootstrap values defined
	Branch lengths: branch lengths are defined
	Horizontal gene transfers: there are HGTs annotated in the tree
	Color ranges: there are color ranges defined
	Auto assigned taxonomy: iTOL's auto taxonomy assigment was used on this tree
	Colored branches: some of the branches have colors defined

Tree functions

You can delete a tree by clicking on the corresponding icon in the tree controls. In addition, there are several functions available in the 'Tree options' menu, which is accessed through the arrow button. You can rename the tree, add more datasets or go to the interactive tree coloring page, where you can define color ranges or assign colors to various branches. In addition, you can access the tree editor, described in more detail below.

Changes to the tree display

When you are logged into your account, and iTOL is displaying a tree which belongs to one of your projects, there will be several new features present in the functions box: Project name will be displayed, and can be clicked to go back to the corresponding workspace. Project navigation buttons will appear, allowing easy navigation to the next and previous tree in the project. The arrow down button will display a popup with links to 10 surrounding trees in the project. The 'saved' link under Views will show a popup with links to all saved views associated with this tree.

Tree editor

The 'Edit tree' function in the tree options popup will take you to the iTOL's interactive tree editor.

The editor's functions, accessed by clicking on a branch or leaf, are described in the table below. After using any of the functions, you should click the 'Update tree' button to preview the changes. Clicking the 'Save tree' button will create the new Newick file and replace the exisiting one. Note that this cannot be undone. You can use the editor to get the tree back to its original state, but the 'Reset tree' will now revert to the last saved state.

Function	Example
Delete a leaf or clade: Selected clade/leaf will be completely removed from the tree.
Collapse a branch: A branch will be removed from the tree. All its children will be transfered to its ancestor branch.
Move a leaf or clade: A clade or leaf will be transfered to the selected target node. Target node will be split in two, and the transfered clade or leaf will become a child of the newly created node.
Reroot the tree on any node: Tree will be re-rooted on the selected node.

Mid-point rooting trees

Using this function, you can re-root the tree using the mid-point approach. Two most distant leaves will be determined, and a point in the middle between them will be used as the new root. After the new root is calculated, you will be able to replace the existing tree with the new version, or create a new copy (keeping the original as well).

Uploading multiple trees in one file

When uploading trees into one of your projects, you can upload multiple trees in one file. Make sure each tree is correctly terminated with a ; (semicolon). Start each tree on a new line. For example, to upload 4 trees into a project:

(A,(B,C));
(D,(E,F));
(G,(H,I));
(J,(K,L));

In addition, you can define tree names and multiple destination projects directly in the tree file. Name can be defined in square brackets directly after the ending semicolon. To define a specific destination project for a tree, use the following syntax for the tree name: tree_name|PROJECT=project_name. Basically, add the 'PROJECT=project_name' after the tree name, and separate it with a vertical line. For example:

(A,(B,C));[Tree_1]
(D,(E,F));[Tree_2|PROJECT=Project_2]
(G,(H,I));[Tree_3]
(J,(K,L));[Tree_4|PROJECT=Project_2]

This would upload 4 trees, each with a defined name (Tree 1, Tree 2,Tree 3,Tree 4). Trees 1 and 3 would end up in the project you started the upload from, and trees 2 and 4 would end up in project named Project 2. Note that Project 2 must already exist in your account, it will NOT be automatically created. If Project 2 did not exist during upload, all the trees will end up in the same project.

Note that spaces in tree and project names should be replaced with underscores (which will automatically be converted back to spaces after upload).