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adaptivemcmc.jl

Useful tools for implementing adaptive MCMC algorithms

advancedmh.jl

A Julia library for random-walk Metropolis-Hastings algorithms

arzwa.github.io

personal website

bayesianhclust

Bayesian hierarchical clustering (~Heller & Ghahramani)

beluga.jl

Statistical analysis of gene family evolution using phylogenetic birth-death processes and WGD inference using rjMCMC

bioalignments.jl

Sequence alignment tools

birthdeathprocesses.jl

(general) birth death processes

deadbird.jl

Statistical analysis of comparative genomic data using phylogenetic birth-death process models

deterministicmixedploidy

Deterministic mixed-ploidy dynamical system

discretemarkovfit.jl

Estimate ESS and posterior model probabilities by fitting a discrete Markov chain to output from a rjMCMC sampler

dotplot

Make a triangular within-genome similarity or homology dotplot using matplotlib

dynamichmc.jl

Implementation of robust dynamic Hamiltonian Monte Carlo methods (NUTS) in Julia.

epabc.jl

Expectation-propagation approximate Bayesian computation

homologizer

Homologizer: phasing gene copies into polyploid subgenomes

i-adhore

i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.

incbetader

ksnotebooks

Notebooks for https://doi.org/10.1016/j.molp.2018.12.019

maeremodel

Approximate Bayesian inference for the genome evolution model of Maere et al. (2005)

martin-lof

papers of Per Martin Löf

morph-bulk

Utilities and CLI for MORPH bulk runs

mscsimplot

Simulate a multispecies coalescent forward in time and make a plot

multilocusisland

newicktree.jl

Newick formatted (phylogenetic) trees

pal2cal

yes indeed

palmtree.jl

Some phylogenetic tree visualization routines

pandoc-templates

Templates for pandoc

pandoc-templates-1

Some templates for Pandoc.

plotthemes.jl

Themes for the Julia plotting package Plots.jl

polystab

py-adhore

Tools for performing I-ADHoRe co-linearity inference and visualization