ARPIP: Ancestral Sequence Reconstruction with Insertions and Deletions under the Poisson Indel Process.

ABSTRACT: Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present-day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here, we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect

SUBMITTER: Jowkar G 

PROVIDER: S-EPMC10275563 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature