Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper posted (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).

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 -distmxout fractid