Journal
BMC BIOINFORMATICS
Volume 12, Issue -, Pages -Publisher
BMC
DOI: 10.1186/1471-2105-12-S1-S15
Keywords
-
Categories
Funding
- MNiSW [N301 065236]
- NSF [0830012, 1017189]
- Division of Computing and Communication Foundations
- Direct For Computer & Info Scie & Enginr [1017189] Funding Source: National Science Foundation
Ask authors/readers for more resources
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 and verified its performance with empirical and simulated data. Conclusions: In test data sets, DrML finds optimal gene duplication and loss scenarios within minutes, even when the gene trees contain sequences from several hundred species. In many cases, these optimal scenarios differ from the lca-mapping that results from a parsimony gene tree reconciliation. Thus, DrML provides a new, practical statistical framework on which to study gene duplication.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available