AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.

ABSTRACT:

Motivation

Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree.

Results

We present AleRax, a software that can infer reconciled gene trees together with a shared species tree using a

SUBMITTER: Morel B 

PROVIDER: S-EPMC10990685 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature