Tree Nine
Put diff files on an existing phylogenetic tree using UShER’s usher sampled task with a bit of help from SRANWRP, followed by conversion of that tree to Taxonium, Newick, and Nextstrain formats. Samples’ SNP distance is calculated and output as a distance matrix, and samples will be placed into clusters based on the distance.
Verified on Terra-Cromwell and miniwdl. Make sure to add `–
This is a companion discussion topic for the original entry at github.com/aofarrel/tree_nine/matUtils_optimize