A LASSO-based approach to sample sites for phylogenetic tree search.

ABSTRACT:

Motivation

In recent years, full-genome sequences have become increasingly available and as a result many modern phylogenetic analyses are based on very long sequences, often with over 100 000 sites. Phylogenetic reconstructions of large-scale alignments are challenging for likelihood-based phylogenetic inference programs and usually require using a powerful computer cluster. Current tools for alignment trimming prior to phylogenetic analysis do not promise a significant reduction in the alignment size and are claimed to have a negative effect on the accuracy of the obtained tree.

Results

Here, we propose an artificial-intelligence-based approach, which provides means to select the optimal subset of sites and a formula by which one can compute the log-likelihood of the entir

SUBMITTER: Ecker N 

PROVIDER: S-EPMC9236582 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature