Nextstrain trees and MicrobeTrace

Nextstrain trees can be downloaded in Newick format and used as input into MicrobeTrace.

When you select for tree branch lengths to be displayed as Divergence, Nextstrain trees show the number of mutations on the x-axis under the tree.

When you download this Newick tree, branch lengths are expressed as the number of mutations between taxa. Use this information to set SNP thresholds in MicrobeTrace. Start by setting the SNP threshold to 6 to see if the network mimics the Newick tree.

Depending on question being asked in the investigation or analysis and how closely related the sequences are in the dataset, you may need to adjust the SNP setting. To do this, open Settings on the main menu, go to Filtering tab, and then increase or decrease the SNP threshold