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Data from: The influence of the number of tree searches on maximum likelihood inference in phylogenomics

Cite this dataset

Shen, Xing-Xing (2024). Data from: The influence of the number of tree searches on maximum likelihood inference in phylogenomics [Dataset]. Dryad. https://doi.org/10.5061/dryad.rv15dv4b7

Abstract

Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., ten) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic inference remains poorly explored. Here, we found that a random starting tree was not as effective as the BioNJ and parsimony starting trees in inferring ML gene tree and that RAxML-NG and PhyML were less sensitive to different starting trees than IQ-TREE. We then examined the effect of the number of tree searches on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree searches on 19,414 gene alignments from 15 animal, plant, and fungal phylogenomic datasets. We found that the number of tree searches substantially impacted the recovery of the best-of-100 ML gene tree topology among 100 searches for a given ML program. In addition, all of the concatenation-based trees were topologically identical if the number of tree searches was ≥ 10. Quartet-based ASTRAL trees inferred from 1 to 80 tree searches differed topologically from those inferred from 100 tree searches for 6 /15 phylogenomic datasets. Lastly, our simulations showed that gene alignments with lower difficulty scores had a higher chance of finding the best-of-100 gene tree topology and were more likely to yield the correct trees.

README

FILE OVERVIEW
The zip folder contains Supplementary Figures S1-S20, Supplementary Tables S1-S6, and Supplementary Text.

File List:
File 1 Name: Supplementary Figures S1-S20.pdf
File 1 Description: This file contains Supplementary Figures S1-S20. Each figure includes its respective legend.
File 2 Name: Supplementary Tables S1-S6.xlsx
File 2 Description: This file contains Supplementary Tables S1-S6. Each table includes its respective title.
File 3 Name: Supplementary_Text.pdf
File 3 Description: This file contains supplementary text detailing the parameters used for each phylogenetic analysis.

Funding

Fundamental Research Funds for the Central Universities, Award: 226-2023-00021