How to use phylot

phyloT automatically generates phylogenetic trees based on the NCBI taxonomy. After parsing the complete NCBI taxonomy, phyloT will generate a pruned tree in the selected format, based on the tree elements you provide. Tree elements can by typed or pasted into the provided input box, or uploaded in a plain text file. You can use any combination of the following element types, separated using commas or newlines:

Click any of the Example buttons below the main input field to see various example tree element combinations.

Searching for a NCBI scientific name

Use the 'Search taxonomy' box to quickly search the full database of NCBI taxonomy names. Each result will show the full scientific name with its taxonomic class and NCBI taxonomy ID. Clicking on any result will append its tax ID to the current tree elements.

Including full clades

phyloT supports generation of full clade trees for any NCBI taxonomy ID or scientific name. To include the complete sub-tree for a NCBI taxonomy ID (or scientific name), simply append a vertical line followed by the keyword "subtree" to the input element.

For example:

Mammalia|subtree
7147|subtree

The example input above would generate a tree containing 2 clades: Mammalia and Insecta (NCBI Tax ID 7147). All NCBI nodes belonging to these clades would be included.

Filtering nodes

In the example above, the final tree would contain ~33 000 nodes, making it hard to manipulate or visualize. phyloT offers two mechanisms for filtering nodes from generated trees:

  1. Interrupting at a specific class

    Using the "Interrupt at" selector, you can specify a taxonomic class where the tree generation will be stopped. For example, if "Genus" is selected, leaves of the included clades will correspond to nodes with taxonomic class genus. Note that this applies only to full clades (ie. nodes appended with keyword "|subtree"). You can still include additional elements corresponding to "higher" taxonomic classes, and these will be present in the tree.

    For example:

    Mammalia|subtree
    7147|subtree
    Escherichia_coli
    

    In the example above, with "Interrupt at" set to Genus, Escherichia coli would still appear as a regular leaf in the tree, even though its class is species (ie. 'higher' than genus).

  2. Removing nodes matching a text pattern

    You can remove all nodes whose scientific names match a certain pattern. Simply type the words and phrases which should be filtered into the Filtering field, separated with commas.

    For example:

    Ascomycota|subtree
    

    In the example above, full Ascomycota phylum tree would contain ~55 000 nodes. However, if various unclassified species and environmental samples are removed, only ~3500 nodes remain. This can be accomplished by entering, for example, "environmental_sample,unclassified" into the Filtering field.

Output options

Node identifiers

When setting the identifier format to "NCBI Taxonomy IDs", all internal nodes of the tree will be prefixed with keyword "INT" (for example, node 7147 will be labeled as INT7147). This is done to prevent various tree parsers from misidentifying these IDs as tree support values (bootstraps).

Collapsing internal nodes

Due to the nature of the underlying NCBI taxonomy data and depending on the provided tree elements, generated trees will often have many internal nodes which have only one child. phyloT therefore offers an option to remove such nodes, by setting the "Internal nodes" option to "Collapsed".

Forcing creation of binary trees

Many nodes in NCBI taxonomy are highly polytomic (have many child branches). If your tree visualization or analysis software requires a strictly binary tree, where each node must have exactly two children, you can set the "Polytomy" option to "No". phyloT will then randomly combine multifurcating nodes into separate bifurcating structures and introduce additional ("fake") internal nodes as required, producing a proper binary tree.

Tree format and file name

In addition to the commonly used Newick format, you can also download the generated trees in NEXUS or phyloXML formats. If a file name is not provided when generating a tree, a randomly generated string will be used.

Visualizing generated trees in iTOL

If you only want to visualize the generated tree, phyloT offers a direct link to iTOL: interactive Tree Of Life. Simply click the "Visualize in iTOL" button. iTOL is an online phylogenetic tree visualization tool, offering powerful annotation features. Check the iTOL website for more details.

User account

Trees created from more than 10 elements require either an active phyloT subscription, institutional access or a tree generation token. Please create a phyloT account first, and then visit your personal info page to view all available options.

Tree generation tokens:

If you don't use phyloT often, tree generation tokens are the simplest solution. They do not expire, and can be purchased directly, or simply obtained by using our sponsor's adverts. Each generated tree requires one token, but you can freely change the phyloT tree options and file format, as long as the tree elements remain the same. Each tree (defined by the tree elements used to generate it) remains freely accessible for 6 months. You can also share our sponsor advert links with your friends. Any tokens generated through those links will be credited to your phyloT account.

Subscription:

phyloT offers monthly or annual subscriptions for unrestricted access. Click the 'Start/extend subscription' button on your personal info page to display the available options. Note that all phyloT subscriptions are non-recurring and will never be extended automatically. Once your subscription expires, you will have to manually reactivate it.

Institutional access:

If your institution currently has a valid phyloT license, you either have direct unrestricted access to phyloT via your IP address, or you were given a phyloT access key. To use a license key, click on the 'Provide access key' button on your personal info page to activate your account. If you are interested in this mode of access, please have your librarian or IT department to obtain a license.