Nextstrain trees and MicrobeTrace

Nextstrain users can now directly view Nextstrain tree data in MicrobeTrace with the click of a button.

• Navigate to the pathogen of your choice on nextstrain.org and display the tree you want.
• Scroll to the bottom with the download options.
• You will see View this dataset on other platforms; click MicrobeTrace.
• The data instantly opens in MicrobeTrace as a 2D network.
• CAVEAT: the tree has to have less than 500 taxa.

CDC users who have their own Nextstrain build on Scicomp will be able to use this feature with their data, since Scicomp has the latest version of Auspice which incorporates the View in MicrobeTrace button.

Alternatively, 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