Related Experiment Video
Updated: Jun 10, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
Published on: July 11, 2025
MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional
Manuel Stark1, Simon A Berger, Alexandros Stamatakis
1Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland.
Background:
Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem.
Results:
Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information.
Conclusions:
We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.
Related Concept Videos
Microbial Phylogeny
Evolutionary Relationships through Genome Comparisons
Modern Molecular Taxonomy
Applications of Molecular Taxonomy
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Phylogenetic Trees

