ConvexML: Fast and accurate branch length estimation under irreversible mutation models, illustrated through applications to CRISPR/Cas9-based lineage tracing.

ABSTRACT: Branch length estimation is a fundamental problem in Statistical Phylogenetics and a core component of tree reconstruction algorithms. Traditionally, general time-reversible mutation models are employed, and many software tools exist for this scenario. With the advent of CRISPR/Cas9 lineage tracing technologies, there has been significant interest in the study of branch length estimation under irreversible mutation models. Under the CRISPR/Cas9 mutation model, irreversible mutations - in the form of DNA insertions or deletions - are accrued during the experiment, which are then read out at the single-cell level to reconstruct the cell lineage tree. However, most of the analyses of CRISPR/Cas9 lineage tracing data have so far been limited to the reconstruction of single-cell tree top

SUBMITTER: Prillo S 

PROVIDER: S-EPMC10705529 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature