Phylogenetic tree

Nextclade Web: download nextclade.auspice.json or nextclade.nwk

Nextclade CLI flags: --output-tree/-T or --output-tree-nwk

Output phylogenetic tree. This is the input reference tree, with query sequences placed onto it during the phylogenetic placement step.

The tree comes either in Auspice JSON v2 format or in Newick format.

Auspice JSON v2 format (description, schema) is the same format that is used by Nextstrain Augur and Auspice packages as well as on And the same as used for the input reference tree in Nextclade. This tree file can be visualized online in or in a local instance of Nextstrain Auspice.

To allow for compatibility with other software, Nextclade can output the tree in Newick format. This is a text-based format for representing phylogenetic trees as nested sets. It is widely used in bioinformatics, but contains only very basic information. It can be viewed online for example on or

⚠️ Note that if alignment or analysis of an individual sequence fails, it cannot participate in phylogenetic placement and is omitted from the output tree. See Errors and warnings section for more details.

⚠️ For CLI users: Note that due to technical limitations of the JSON format, it cannot be streamed entry-by entry, i.e. before writing the output to the file, all entries need to be accumulated in memory. If the tree output is requested (through --output-tree or --output-all arguments), for large input data, it can cause very high memory consumption, disk swapping, decreased performance and crashes. Consider removing this output for large input data, running on a machine with more RAM, or processing data in smaller chunks.

⚠️ Note, all positions are in alignment coordinates and after all the insertions stripped.