treePL: divergence time estimation using penalized likelihood for large phylogenies

treePL: divergence time estimation using penalized likelihood for large phylogenies

UNLABELLED Ever larger phylogenies are being constructed due to the explosion of genetic data and development of high-performance phylogenetic reconstruction algorithms. However, most methods for calculating divergence times are limited to datasets that are orders of magnitude smaller than recently published large phylogenies. Here, we present an algorithm and implementation of a divergence tim...

Penalized Bregman Divergence Estimation via Coordinate Descent

Variable selection via penalized estimation is appealing for dimension reduction. For penalized linear regression, Efron, et al. (2004) introduced the LARS algorithm. Recently, the coordinate descent (CD) algorithm was developed by Friedman, et al. (2007) for penalized linear regression and penalized logistic regression and was shown to gain computational superiority. This paper explores...

Penalized Likelihood Density Estimation :

Estimating divergence times in large molecular phylogenies.

Molecular dating of species divergences has become an important means to add a temporal dimension to the Tree of Life. Increasingly larger datasets encompassing greater taxonomic diversity are becoming available to generate molecular timetrees by using sophisticated methods that model rate variation among lineages. However, the practical application of these methods is challenging because of th...

Improved estimation of site occupancy using penalized likelihood.

When detection or occupancy probability is small or when the number of sites and number of visits per site is small, maximum likelihood estimators (MLE) of site occupancy parameters have large biases, are numerically unstable, and the corresponding confidence intervals have smaller than nominal coverage. We propose an alternative method of estimation, based on penalized likelihood. This method ...