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ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning.

Abstract：

:Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they are not always feasible, and sometimes depend on preliminary assumptions which do not hold for sequence data. Moreover, although these methods are dedicated to revealing the processes that underlie the sequence data, they do not always produce the most accurate trees. Notably, phylogeny reconstruction consists of two related tasks, topology reconstruction and branch-length estimation. It was previously shown that in many cases the most complex model, GTR+I+G, leads to topologies that are as accurate as using existing model selection criteria, but overestimates branch lengths. Here, we present ModelTeller, a computational methodology for phylogenetic model selection, devised within the machine-learning framework, optimized to predict the most accurate nucleotide substitution model for branch-length estimation. We demonstrate that ModelTeller leads to more accurate branch-length inference than current model selection criteria on data sets simulated under realistic processes. ModelTeller relies on a readily implemented machine-learning model and thus the prediction according to features extracted from the sequence data results in a substantial decrease in running time compared with existing strategies. By harnessing the machine-learning framework, we distinguish between features that mostly contribute to branch-length optimization, concerning the extent of sequence divergence, and features that are related to estimates of the model parameters that are important for the selection made by current criteria.

journal_name

Mol Biol Evol

journal_title

Molecular biology and evolution

authors

Abadi S,Avram O,Rosset S,Pupko T,Mayrose I

doi

10.1093/molbev/msaa154

subject

Has Abstract

pub_date

2020-11-01 00:00:00

pages

3338-3352

issue

eissn

0737-4038

issn

1537-1719

pii

5862639

journal_volume

pub_type

杂志文章

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ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning.