swMATH ID: 38915
Software Authors: Stark, M., Berger, S., Stamatakis, A., von Mering, C.
Description: MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. 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.
Homepage: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-461
Source Code:  https://github.com/meringlab/mltreemap
Related Software: SEPP; FastTree; pplacer; DEPP; PhyloGeoTool; INSTRAL; UShER; HmmUFOtu; Scoredist; TIPP; ASTRAL-II; BIONJ; APPLES; EPA-ng; PhyloSift; iGTP; ProtTest 3; MrBayes; Gegenees; POY
Cited in: 3 Publications

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