Name: Arthur Zwaenepoel
Type: User
Company: https://eep.univ-lille.fr/en/presentation-english/
Bio: Evolutionary and computational biology, currently a postdoc in the speciation group at Université de Lille.
Blog: https://arzwa.github.io/
Arthur Zwaenepoel's Projects
Useful tools for implementing adaptive MCMC algorithms
A Julia library for random-walk Metropolis-Hastings algorithms
personal website
Bayesian hierarchical clustering (~Heller & Ghahramani)
Statistical analysis of gene family evolution using phylogenetic birth-death processes and WGD inference using rjMCMC
Sequence alignment tools
(general) birth death processes
Statistical analysis of comparative genomic data using phylogenetic birth-death process models
Deterministic mixed-ploidy dynamical system
Estimate ESS and posterior model probabilities by fitting a discrete Markov chain to output from a rjMCMC sampler
Make a triangular within-genome similarity or homology dotplot using matplotlib
Implementation of robust dynamic Hamiltonian Monte Carlo methods (NUTS) in Julia.
Expectation-propagation approximate Bayesian computation
Homologizer: phasing gene copies into polyploid subgenomes
i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.
Notebooks for https://doi.org/10.1016/j.molp.2018.12.019
Approximate Bayesian inference for the genome evolution model of Maere et al. (2005)
papers of Per Martin Löf
Utilities and CLI for MORPH bulk runs
Simulate a multispecies coalescent forward in time and make a plot
Newick formatted (phylogenetic) trees
yes indeed
Some phylogenetic tree visualization routines
Templates for pandoc
Some templates for Pandoc.
Themes for the Julia plotting package Plots.jl
Tools for performing I-ADHoRe co-linearity inference and visualization