Other phylogenetic trees
iTOL is used to generate trees in various projects. Some examples include:
- SmashCommuinty
- iPath: interactive Pathways Explorer
- metaTIGER: Metabolic Gene Evolution Resource
- eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups
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 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'
- Uniprot protein IDs or accession numbers: protein IDs will appear as leaves in the generated tree, while the clades will be NCBI taxonomy IDs. If multiple IDs map to the same species, they will all be grouped into a multifurcating clade
- NCBI protein accession numbers: same as above
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:
- Sub-tree generation can 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).
- You can remove all nodes whose names match a certain patters. Filtering is activated by adding the "-filter:" keyword to the end of the |subtree command. After the keyword, add the words and phrases which should be filtered, separated with commas. Replace spaces with underscores in multiword phrases. For example, if you specify "Ascomycota|subtree-genus-filter:environmental_sample,unclassified", Ascomycota sub-tree will be interrupted at genus level, and all nodes which contain the words "unclassified" or "environmental sample" will be removed.
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:
- ncbi_complete_with_taxIDs.newick.gz: complete tree, using taxonomy IDs
- ncbi_complete_with_names.newick.gz: complete tree, using scientific names
- ncbi_complete_collapsed_with_taxIDs.newick.gz: complete tree, using taxonomy IDs; internal nodes with only one child are removed
- ncbi_complete_collapsed_with_names.newick.gz: complete tree, using scientific names; internal nodes with only one child are removed
Examples
Click the links to preload the form with example queires:
- 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
- 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
- Ascomycota sub-tree, interrupted at genus level : fill the form
- Same as above, but with unclassified species and environmental samples removed : fill the form
