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bioRxiv · 10.1101/734848

A Fast and Memory-Efficient Implementation of the Transfer Bootstrap

Lutteropp, S.·Kozlov, A. M.·Stamatakis, A.
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Abstract

Recently, Lemoine et al. suggested the Transfer Bootstrap Expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support metric on taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Therefore, we developed a fast and memory-efficient TBE implementation. We improved upon the original algorithm described by Lemoine et al. by introducing multiple algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10x - 40x memory savings compared to booster. Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallelized version that also computes additional TBE-related statistics is available in pll-modules and RAxML-NG forks at: https://github.com/lutteropp/pll-modules/tree/tbe and https://github.com/lutteropp/raxml-ng/tree/tbe.

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Lutteropp, S., Kozlov, A. M., Stamatakis, A.. 2019-08-20. A Fast and Memory-Efficient Implementation of the Transfer Bootstrap. https://doi.org/10.1101/734848

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