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.

A computational analysis of Gondi dialectal classification

Simulate predictive datasets from MrBayes' output

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

Testing effects of missing data on phylogenetic inferences

This repository contains some phylogenetic trees I have done for practical purposes.

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.

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

Automatic Detection of Positively Selected Sites

Runs MrBayes on multiple loci in parallel

This project performs an automated phylogenetic analysis of nucleotide sequences retrieved from NCBI. The pipeline includes sequence alignment, concatenation, phylogenetic inference (maximum likelihood, maximum parsimony, and Bayesian), and formatting for visualization.

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