mrbayes

Archaeopteryx.js is a software tool for the visualization and analysis of highly annotated phylogenetic trees.

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

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

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.

GUI and CLI workflow for phylogenetic tree construction, tanglegram comparison, and optional Foldseek protein-structure similarity.

Structure-informed phylogenomic census of the Sm/Lsm/Hfq superfamily: DPANN/Asgard archaea retain the Sm fold while the bacterial CPR radiation has lost it

Rooted, dual-method (ML + Bayesian) phylogeny of the bacterial Hfq family, with archaeal SmAP outgroup rooting and ESMFold/Foldseek structural verification

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

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

The fate of the Sm fold under genome reduction: a structure-informed three-domain phylogeny showing repeated bacterial Hfq loss vs archaeal Sm/Lsm retention