Taxonomic level

Biological：iPhylo trees show the taxonomic structure in 8 main taxonomic ranks: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species level of NCBI taxonomy database.

If the node entered is outside of these ranks, e.g. subfamily, iPhylo will keep your node and provide the parent main rank above this rank.

Chemical: The resulting chemical classification tree is organized around chemical taxonomy, starting from the highest level and descending to the lowest level: Kingdom, SuperClass, Class, SubClass, Parent Level 1, and Parent Level 2. The last two categories represent two taxonomic levels directly below SubClass.

Branch length

iPhylo tree don’t contain branch length information or support value, however you can set all branch length to 1.00000 for visual clarity and subsequent analysis in external software.

Nodes

All nodes in the biological tree are labeled with scientific names.

The leaf nodes (the last node of each branch) of the chemical tree are labeled with ids, and the other internal nodes are labeled with compound category names, like "Glycerolipids". Don't worry about figuring out which compounds the ids correspond to, we'll provide a table of correspondences.

Use the "Interrupt at" selection box to interrupt the extension of a tree branch at any specific taxonomy level. This function will significantly avoid the formation of excessively large trees with an overwhelming number of nodes.

You can quickly obtain a full-clade tree for any taxonomic level using the operator |subtree. For example:

This feature in chemical classification tree needs to input the chemical category names as the prefixes. For example:

Input format

Either paste in the "Tree elements" input box or upload a plain text file.

Input element

You can use the following element types, or any combination of them. Elements should be separated by comma or new line.

Biological:

• Organism names: The names are flexible as long as they are indexed in the NCBI taxonomic database, such as "scientific name", "synonym", or "common name". For example, "human" can serve as the common name for "Homo sapiens". All leaf nodes within the iPhylo trees will be their corresponding scientific name. You can see how name changed in the output text file. For instance:

  honey bee -> Apis mellifera

  house mouse -> Mus musculus

  human -> Homo sapiens

• Taxonomy identifiers (taxID)
• Subtree: Follows the format "xxx|subtree", see details in Full-clade trees.

Chemical:

• InChIKey: We strongly recommend using InChIKey to represent chemicals due to its uniqueness and conciseness. Other formats may lack complete information in the database.

• SMILES: If you use SMILES to represent compounds, please input them via plain text, separating each by a new line.

• InChI: If you use InChI to represent compounds, please input them via plain text, separating each by a new line.

• Subtree: Follows the format "xxx|subtree", see details in Full-clade trees.

We assign "iphylo_tree" or "ichem_tree" as the default tree name for biological and chemical tree respectively. However, feel free to modify these names to your preference.

Branch Length

Select "True" to standardize all branch lengths to 1.00000. If "False" is chosen, the resulting tree will lack branch length information.

Format

Opt to download the result tree in NEXUS, Newick or phyloXML formats. The TXT format is mandatory for download.

ASCII Tree: Simple pretty-printing of your tree structures using pure ASCII characters for drawing branches and edges.

For instance:

                      _____ ____ _____ ____ _____ _____ s__Drosophila_melanogaster
                     |
           _____ ____|           _____ ____ _____ _____ s__Mus_musculus
          |          |      ____|
          |          |_____|    |_____ ____ _____ _____ s__Homo_sapiens
    ______|                |
          |                |____ _____ ____ _____ _____ s__Gallus_gallus
          |
          |_____ ____ _____ ____ _____ ____ _____ _____ s__Escherichia_coli
                                

Additional files:

When running iPhylo, we generate some other files to help you understand the tree better:

• iphylo_tree_items.csv, ichem_tree_items.csv

These spreadsheet enlist the taxID (id for chemicals), scientific name (name, InChI, InChIKey, SMILES for chemicals) and lineage for the taxa you input.

• iphylo_tree_items_for_anno.csv

Similar to iphylo_tree_items.csv, but tailored for iPhylo Visual, serves as an annotation for basic visualization of tree leaves. It can be directly uploaded to iPhylo Visual for enhanced visualization and annotation.

• no_match_result.txt

This file is used to alert you when you have input taxIDs and names that are not in the NCBI taxonomy database, or when you have input a name that corresponds to more than one taxID. Note that the taxID is the unique identifier for NCBI taxonomy database entries.

In the case of chemical trees, this file is used to indicate which compounds are not in the iPhylo database or are missing classification information. Our database mainly contains functional compounds, if you want more more compounds information, try our iPhylo CLI chemoline module.