A computational analysis of Gondi dialectal classification

A collection of phylogenetics tutorials delivered to colleagues at the Centre for Biological Control (CBC). Topics include producing Bayesian and Maximum Likelihood trees, haplotype networks, reading phylogenies into R, analysing ISSR and SSR data, and using STRUCTURE and SplitsTree.

Simulate predictive datasets from MrBayes' output

Testing effects of missing data on phylogenetic inferences

The PKS Test software was designed to directly verify whether a phylogeny is clock-like following a Poisson law.

Runs MrBayes on multiple loci in parallel

Below is the code of our thesis: A Three-Level Parallel Algorithm Using AVX For MrBayes 3.2. Mingjie Zhao did most of the work, and I am glad that I did make some contributions to performance optimization.

Automatic Detection of Positively Selected Sites

A shiny app to summarize and evaluate the results of Bayesian phylogenetic analyses

A python pipeline that brings together tools for generation of consensus sequence, multiple sequence alignment, and phylogenetic analysis.