Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.

ABSTRACT:

Background

The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding the mapping that minimizes the number of duplication and loss events. Probabilistic modeling of gene duplication and loss is relatively new and has largely focused on birth-death processes.

Results

We introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths. We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model. We implemented the algorithm in the program DrML a

SUBMITTER: Gorecki P 

PROVIDER: S-EPMC3044269 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature