• Publications
  • Influence
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
AVILABILITY BUCKy is a C++ program that implements Bayesian concordance analysis that uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concords from clades supported by the largest proportions of genes. Expand
Bayesian estimation of concordance among gene trees.
A novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods and introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees. Expand
General predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes, showing that these tests are more powerful than existing tests using standardized contrasts. Expand
A linear-time algorithm for Gaussian and non-Gaussian trait evolution models.
  • L. Ho, C. Ané
  • Mathematics, Medicine
  • Systematic biology
  • 1 May 2014
We developed a linear-time algorithm applicable to a large class of trait evolution models, for efficient likelihood calculations and parameter inference on very large trees. Our algorithm solves theExpand
Prospects for Building the Tree of Life from Large Sequence Databases
An analysis of two “supermatrices” suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life. Expand
The iPlant Collaborative: Cyberinfrastructure for Plant Biology
These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services. Expand
Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting
This work presents a statistical method to infer phylogenetic networks from multi-locus genetic data in a pseudolikelihood framework and applies it to reconstruct the evolutionary relationships among swordtails and platyfishes, which is characterized by widespread hybridizations. Expand
Rphylopars: fast multivariate phylogenetic comparative methods for missing data and within‐species variation
1.Over the past several years, phylogenetic comparative studies have increasingly approached trait evolution in a multivariate context, with a number of taxa that continues to rise dramatically.Expand
Fast and accurate detection of evolutionary shifts in Ornstein–Uhlenbeck models
A phylogenetic lasso method to study trait evolution from comparative data and detect past changes in the expected mean trait values, using the Ornstein–Uhlenbeck process, which can model a changing adaptive landscape over time and over lineages. Expand
Covarion structure in plastid genome evolution: a new statistical test.
Two new tests for covarion evolution are described and demonstrated with simulations that they perform well under a wide range of conditions and are likely due to changes in the selective constraints of amino acids. Expand