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USEARCH v11

tree2distmx command

Calculates a a distance matrix from a tree in Newick format, which must have branch lengths specified. The distance between two leaf nodes in the tree is calculated as the sum over branch lengths of the shortest path between leaves.

The distance matrix is written to the filename given by the -distmxout option. See distance matrix for format options.

Example

usearch -tree2distmx tree,phy -distmxout mx.txt -format tabbed_pairs -distmxo fractid