Data on the solution and processing time reached when constructing a phylogenetic tree using a quantum-inspired computer

Wataru Onodera, Nobuyuki Hara, Shiho Aoki, Toru Asahi, Naoya Sawamura*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Phylogenetic trees provide insight into the evolutionary trajectories of species and molecules. However, because (2n-5)! Phylogenetic trees can be constructed from a dataset containing n sequences, but this method of phylogenetic tree construction is not ideal from the viewpoint of a combinatorial explosion to determine the optimal tree using brute force. Therefore, we developed a method for constructing a phylogenetic tree using a Fujitsu Digital Annealer, a quantum-inspired computer that solves combinatorial optimization problems at a high speed. Specifically, phylogenetic trees are generated by repeating the process of partitioning a set of sequences into two parts (i.e., the graph-cut problem). Here, the optimality of the solution (normalized cut value) obtained by the proposed method was compared with the existing methods using simulated and real data. The simulation dataset contained 32–3200 sequences, and the average branch length according to a normal distribution or the Yule model ranged from 0.125 to 0.750, covering a wide range of sequence diversity. In addition, the statistical information of the dataset is described in terms of two indices: transitivity and average p-distance. As phylogenetic tree construction methods are expected to continue to improve, we believe that this dataset can be used as a reference for comparison and confirmation of the validity of the results. Further interpretation of these analyses is explained in W. Onodera, N. Hara, S. Aoki, T. Asahi, N. Sawamura, Phylogenetic tree reconstruction via graph cut presented using a quantum-inspired computer, Mol. Phylogenet. Evol. 178 (2023) 107636.

Original languageEnglish
Article number108970
JournalData in Brief
Publication statusPublished - 2023 Apr


  • Distance-matrix method
  • Graph cut
  • Phylogenetic reconstruction
  • Quantum-inspired computing

ASJC Scopus subject areas

  • General


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