Fast tumor phylogeny regression via tree-structured dual dynamic programming.

ABSTRACT:

Motivation

Reconstructing the evolutionary history of tumors from bulk DNA sequencing of multiple tissue samples remains a challenging computational problem, requiring simultaneous deconvolution of the tumor tissue and inference of its evolutionary history. Recently, phylogenetic reconstruction methods have made significant progress by breaking the reconstruction problem into two parts: a regression problem over a fixed topology and a search over tree space. While effective techniques have been developed for the latter search problem, the regression problem remains a bottleneck in both method design and implementation due to the lack of fast, specialized algorithms.

Results

Here, we introduce fastppm, a fast tool to solve the perfect phylogeny regression problem via tree-str

SUBMITTER: Schmidt H 

PROVIDER: S-EPMC12261417 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature