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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.
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.
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.