Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap
نویسندگان
چکیده
منابع مشابه
Penalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap.
The increasing diversity and heterogeneity of molecular data for phylogeny estimation has led to development of complex models and model-based estimators. Here, we propose a penalized likelihood (PL) framework in which the levels of complexity in the underlying model can be smoothly controlled. We demonstrate the PL framework for a four-taxon tree case and investigate its properties. The PL fra...
متن کاملParsimony, likelihood, and simplicity
The latest charge against parsimony in phylogenetic inference is that it involves estimating too many parameters. The charge is derived from the fact that, when each character is allowed a branch length vector of its own (instead of the homogeneous branch lengths assumed in current likelihood models), the results for likelihood and parsimony are identical. Parsimony, however, can also be derive...
متن کاملCount: evolutionary analysis of phylogenetic profiles with parsimony and likelihood
SUMMARY Count is a software package for the analysis of numerical profiles on a phylogeny. It is primarily designed to deal with profiles derived from the phyletic distribution of homologous gene families, but is suited to study any other integer-valued evolutionary characters. Count performs ancestral reconstruction, and infers family- and lineage-specific characteristics along the evolutionar...
متن کاملMaximum likelihood, profile likelihood, and penalized likelihood: a primer.
The method of maximum likelihood is widely used in epidemiology, yet many epidemiologists receive little or no education in the conceptual underpinnings of the approach. Here we provide a primer on maximum likelihood and some important extensions which have proven useful in epidemiologic research, and which reveal connections between maximum likelihood and Bayesian methods. For a given data set...
متن کاملMaximum Likelihood Methods for Phylogenetic Inference
In this article, we provide an overview of maximum likelihood methods for phylogenetic inference. A brief introduction to general maximum likelihood estimation is provided. We define a phylogenetic likelihood, summarize how to compute this likelihood, and then discuss approaches used to maximize the phylogenetic likelihood function. We discuss a property of the maximum likelihood estimation, ca...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Systematic Biology
سال: 2008
ISSN: 1076-836X,1063-5157
DOI: 10.1080/10635150802422274