EMDUniFrac: exact linear time computation of the UniFrac metric and identification of differentially abundant organisms

DOI10.1007/s00285-018-1235-9zbMath1398.92016arXiv1611.04634OpenAlexW2952999494WikidataQ88462707 ScholiaQ88462707MaRDI QIDQ1784414

David Koslicki, Jason McClelland

Publication date: 26 September 2018

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1611.04634

zbMATH Keywords

optimizationlinear spacelinear timeKantorovich-Rubinstein metricEarth movers distanceUniFrac

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) General biostatistics (92B15) Ecology (92D40) Software, source code, etc. for problems pertaining to biology (92-04)

Related Items (1)

EMDUnifrac

Uses Software

• Python
• EMD
• ETE
• GitHub

Cites Work

• Monge and feasibility sequences in general flow problems
• A polynomial time primal network simplex algorithm for minimum cost flows
• The earth mover's distance as a metric for image retrieval
• The Phylogenetic Kantorovich–Rubinstein Metric for Environmental Sequence Samples
• Face Recognition Using Spatially Constrained Earth Mover's Distance

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