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From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses

View ORCID ProfileJulia Haag, Dimitri Höhler, View ORCID ProfileBen Bettisworth, View ORCID ProfileAlexandros Stamatakis
doi: https://doi.org/10.1101/2022.06.20.496790
Julia Haag
1Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
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  • For correspondence: julia.haag@h-its.org
Dimitri Höhler
1Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
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Ben Bettisworth
1Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
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Alexandros Stamatakis
1Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
2Institute for Theoretical Informatics, Karlsruhe Insititute of Technology, 76131 Karlsruhe, Germany
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Abstract

Phylogenetic analyses under the Maximum Likelihood model are time and resource intensive. To adequately capture the vastness of tree space, one needs to infer multiple independent trees. On some datasets, multiple tree inferences converge to similar tree topologies, on others to multiple, topologically highly distinct yet statistically indistinguishable topologies. At present, no method exists to quantify and predict this behavior. We introduce a method to quantify the degree of difficulty for analyzing a dataset and present Pythia, a Random Forest Regressor that accurately predicts this difficulty. Pythia predicts the degree of difficulty of analyzing a dataset prior to initiating Maximum Likelihood based tree inferences. Pythia can be used to increase user awareness with respect to the amount of signal and uncertainty to be expected in phylogenetic analyses, and hence inform an appropriate (post-)analysis setup. Further, it can be used to select appropriate search algorithms for easy-, intermediate-, and hard-to-analyze datasets.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted June 21, 2022.
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From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses
Julia Haag, Dimitri Höhler, Ben Bettisworth, Alexandros Stamatakis
bioRxiv 2022.06.20.496790; doi: https://doi.org/10.1101/2022.06.20.496790
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From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses
Julia Haag, Dimitri Höhler, Ben Bettisworth, Alexandros Stamatakis
bioRxiv 2022.06.20.496790; doi: https://doi.org/10.1101/2022.06.20.496790

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