arzwa

wgd

Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd.

Whale.jl

Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation

Beluga.jl

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

NewickTree.jl

Newick formatted (phylogenetic) trees

TaoNet

Simulate gene family syntenic networks.

whaleprep

Nextflow pipeline for preparatory analyses for Whale

py-adhore

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

DeadBird.jl

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

TwoTypeDLModel

Inference for a two type continuous-time branching process model of gene family evolution

IncBetaDer

morph-bulk

Utilities and CLI for MORPH bulk runs

AdvancedMH.jl

A Julia library for random-walk Metropolis-Hastings algorithms

arzwa.github.io

personal website

BayesianHClust

Bayesian hierarchical clustering (~Heller & Ghahramani)

BioAlignments.jl

Sequence alignment tools

DeterministicMixedPloidy

Deterministic mixed-ploidy dynamical system

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

MaereModel

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

MSCSimPlot

Simulate a multispecies coalescent forward in time and make a plot

MultilocusIsland

pandoc-templates-1

Some templates for Pandoc.

PlotThemes.jl

Themes for the Julia plotting package Plots.jl

PolyStab

revbayes

Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

SmoothTree.jl

Bayesian estimation of conditional clade distributions etc.

vimwiki_markdown

vimwiki markdown file to html with syntax highlighting.

vuilbak.github.io

vuilbak website

WrightDistribution