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Felsenstein confidence

The Felsenstein bootstrap compares a tree against a resampled ensemble of trees. Confidence of an edge is calculated as the fraction of trees in the ensemble having an exactly matching edge. Edges match if they induce the same bipartition of leaf labels.

Confidence can also be calculated using transfer expectation.

Reference

Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 422 39, 783-791 (1985).

120,000 new RNA virus species discovered by mining the SRA (paper).

Syncmers are better than minimizers (paper).

Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper (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).