Reference tree

Nextclade Web (advanced mode): accepted in “Reference tree” drag & drop box. A remote URL is also accepted in input-tree URL parameter.

Nextclade CLI argument: --input-tree/-a

Accepted formats: Auspice JSON v2 (description, schema) - this is the same format that is used in Nextstrain. It is produced by augur export and consumed by Nextstrain Auspice. Refer to Nextstrain documentation at https://docs.nextstrain.org and in particular the augur documentation on how to build your own trees. Using augur to make the reference tree is not a strict requirement, however the output tree must follow the Auspice JSON v2 schema.

The phylogenetic reference tree which serves as a target for phylogenetic placement (see Algorithm: Phylogenetic placement). Nearest neighbor information is used to assign clades (see Algorithm: Clade Assignment) and to identify private mutations, including reversions.

The tree must be rooted at the sample that matches the reference sequence. A workaround in case one does not want to root the tree to be rooted on the reference is to attach the mutational differences between the tree root and the reference on the branch leading to the root node. This can be accomplished by passing the reference sequence to augur ancestral’s --root-sequence argument (see the augur ancestral docs).

The tree must contain a clade definition for every node (including internal): every node must have a value at node_attrs.clade_membership (although it can be an empty string).

The tree should be sufficiently large and diverse to meet clade assignment expectations of a particular use-case, study or experiment. Only clades present on the reference tree can be assigned to query sequences.

💡 Nextclade CLI supports file compression and reading from standard input. See section Compression, stdin for more details.