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bioRxiv · 10.1101/2022.10.26.513936

BATCH-SCAMPP: Scaling phylogenetic placement methods to place many sequences

Wedell, E.·Shen, C.·Warnow, T.
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Abstract

Phylogenetic placement, the problem of placing sequences into phylogenetic trees, has been limited either by the number of sequences placed in a single run or by the size of the placement tree. The most accurate scalable phylogenetic placement method with respect to the number of query sequences placed, EPA-ng, has a runtime that scales sublinearly to the number of query sequences. However, larger phylogenetic trees cause an increase in EPA-ngs memory usage, limiting the method to placement trees of up to 10,000 sequences. Our recently designed SCAMPP framework has been shown to scale EPA-ng to larger placement trees of up to 200,000 sequences by building a subtree for the placement of each query sequence. The approach of SCAMPP does not take advantage of EPA-ngs parallel efficiency since it only places a single query for each run of EPA-ng. Here we present BATCH-SCAMPP, a new technique that overcomes this barrier and enables EPA-ng and other phylogenetic placement methods to scale to ultra-large backbone trees and many query sequences. BATCH-SCAMPP is freely available at https://github.com/ewedell/BSCAMPP_code.

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Wedell, E., Shen, C., Warnow, T.. 2022-10-27. BATCH-SCAMPP: Scaling phylogenetic placement methods to place many sequences. https://doi.org/10.1101/2022.10.26.513936

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