Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.

ABSTRACT: ALE and GeneRax are tools for probabilistic gene tree-species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simula

SUBMITTER: Williams TA 

PROVIDER: S-EPMC10373948 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature