Other phylogenetic trees

iTOL is used to generate trees in various projects. Some examples include:

If you're interested or need help in using iTOL for your own large scale display of various trees, feel free to contact us.

Tree generator based on NCBI Taxonomy

Use this form to automatically generate a phylogenetic tree based on the full NCBI taxonomy tree. After parsing the complete NCBI taxonomy, iTOL will generate the pruned tree in Newick format, based on the information you provide. You can use the following:

NCBI taxonomy IDs: they will appear as leaves in the generated tree, regardless of their taxonomic class. Classes can be mixed freely, ie. one ID can represent a species and another a phylum
NCBI scientific names: make sure you provide the proper NCBI scientific name (including proper capitalization) and replace all spaces with underscores ('_'). For example, human should be specified using 'Homo_sapiens'

Our tree generator also supports generation of complete sub-trees for any NCBI taxonomy ID. To create a sub-tree for a NCBI taxonomy ID (or scientific name), simply append a vertical line followed by the keyword "subtree" (for example "Mammalia|subtree"). Sub-tree generation can also be interrupted at a specific NCBI taxonomic classes. Interruption is activated by appending the "|subtree" keyword with a dash and desired NCBI taxonomic class where sub-tree generation should stop. For example, if you specify "Mammalia|subtree-genus", leaves of the generated tree will correspond to nodes with class genus (such as Homo).

Unlimited number of sub-trees and regular taxnomy IDs or names can be specified at the same time.

Examples

Click the links to preload the form:

A simple 5 species tree, specified as scientific names: fill the form
Same as 1. above, but with taxonomy IDs: fill the form
A sub-tree of all mammalian taxa in NCBI: fill the form
Same as 3. above, but interrupted at genus level : fill the form
Same as 4. above, adding a sub-tree of all insect taxa (note that the genus filter will also be applied to insect taxa, even though it was not specified directly): fill the form
Same as 5. above, adding E.coli as an outlier : fill the form

NCBI taxa (IDs or names):	Upload a file with taxa (IDs or names):
	You can provide any number of NCBI taxa, separated by newlines. They do not have to belong to the same taxonomic category. If some of the IDs are changed in the current NCBI version, they will be automatically replaced with the correct new versions.

NCBI taxa (IDs or names):

Upload a file with taxa
(IDs or names):

You can provide any number of NCBI taxa, separated by newlines. They do not have to belong to the same taxonomic category. If some of the IDs are changed in the current NCBI version, they will be automatically replaced with the correct new versions.