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MSClust | A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence

An adaptive multi-seeds based heuristic clustering method that avoids the large memory need for storing seeds and/or distance matrix. MSClust uses a greedy heuristic strategy to build one cluster at a time. Each cluster is expanded from a limited initial set with multi-seeds, where the initial multi-seeds are generated based on an adaptive strategy. Unassigned sequences are then compared to the seeds sequentially. A new sequence is added to the current cluster and removed from the input if the average distance between the sequence and seeds is smaller than the user-defined threshold; otherwise, the sequence is marked as unassigned.

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MSClust classification

MSClust specifications

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Multi-Seeds based Clustering algorithm
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MSClust distribution


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MSClust support


  • Hongyu Zhao <>


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College of Automation, Northwestern Polytechnical University, XI'an, China; Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA; Keck Biotechnology Laboratory, Biostatistics Resource, Yale School of Medicine, New Haven, CT, USA

Funding source(s)

This work was supported in part by NIH GM59507, UL1 RR024139, National Natural Science Foundation of China (No. 61170134), Aeronautical Science Foundation of China (No.20100853010) and Doctorate Foundation of Northwestern Polytechnical University (No. cx201017).

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