Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem

Algorithms Mol Biol. 2024 Jan 8;19(1):2. doi: 10.1186/s13015-023-00249-9.ABSTRACTThe last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem for the Dollo criterion score in [Formula: see text] time, where n is the number of leaves, k is the number of characters, and [Formula: see text] is the set of clades used as constraints. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. This motivated us to implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility for analyzing retroelement inserti...
Source: Algorithms for Molecular Biology : AMB - Category: Molecular Biology Authors: Source Type: research