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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 any combination of the following ID types:

NCBI Node sub-trees

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").

Filtering the sub-trees

When using the sub-tree generation feature, you tree might get cluttered by unwanted nodes. Examples include various environmental sequences and unclassified species/strains. You can filter the subtrees in two ways:

Unlimited number of sub-trees, filters, regular taxnomy IDs, scientific names and protein IDs/ACCs can be specified at the same time.

Please remember that trees generated using the form below simply represent pruned versions of NCBI taxonomy, nothing more. NO proper phylogenetic tree reconstruction methods were used in their creation, and they CANNOT have proper branch lengths or boostrap values.

Complete NCBI taxonomy in Newick format

If you are interested in a dump of complete NCBI taxonomy in Newick format, we provide four different versions for download:

Examples

Click the links to preload the form with example queires:

  1. A simple 5 species tree, specified as scientific names: fill the form
  2. Same as 1. above, but with taxonomy IDs: fill the form
  3. A sub-tree of all mammalian taxa in NCBI: fill the form
  4. Same as 3. above, but interrupted at genus level : fill the form
  5. 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
  6. Same as 5. above, adding E.coli as an outlier : fill the form
  7. A simple tree with 5 proteins from 3 species. There are 3 NCBI protein ACCs, one Uniprot ID (TITIN_HUMAN) and one Uniprot ACC (Q3UT48): fill the form
  8. Ascomycota sub-tree, interrupted at genus level : fill the form
  9. Same as above, but with unclassified species and environmental samples removed : fill the form

ID selection:Upload a file with IDs:

You can provide any number of NCBI taxa, names or protein IDs/ACCs, 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.