Phylogenetic Analysis and Intraspecific Variation: Performance of Parsimony, Likelihood, and Distance Methods

Phylogenetic analysis and intraspecific variation: performance of parsimony, likelihood, and distance methods.

Intraspecific variation is abundant in all types of systematic characters but is rarely addressed in simulation studies of phylogenetic method performance. We compared the accuracy of 15 phylogenetic methods using simulations to (1) determine the most accurate method(s) for analyzing polymorphic data (under simplified conditions) and (2) test if generalizations about the performance of phylogen...

Count: 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...

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence align...

Phylogenetic inference and parsimony analysis.

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...