ammodramus

mope

Infer the dynamics of mitochondrial heteroplasmy during different life stages using population genetics and phylogenetics

coalseam

Simulating coalescence through population pedigrees

discoal

(fork with minor changes to output) discoal is a coalescent simulation program capable of simulating model with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples. This is a minor fork that changes the output slightly.

tsmc

triploid SMC inference method

alnclst

A simple UCLUST-like clustering algorithm for pre-aligned sequences with built in recentering

ammodramus.github.io

angsd

Program for analysing NGS data.

ebsom

Empirical Bayes somatic variant calling

opl

Analysis scripts and notebooks accompanying a paper on mitochondrial heteroplasmy in humans

R-labs

Introduction to (base) R for biologists

demographic_lstm

hair

analysis of mtDNA heteroplasmy in hair samples

infsites

A program to calculate exact sampling probabilities under the infinite sites mutation model in one or two demes

jupyter-vim-binding

Jupyter meets Vim. Vimmer will fall in love.

microplink

Fast and minimal PLINK file processing with numba

NCBI_taxonomy_tree

NCBI taxonomy tree in-memory mapping

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

wrightfishersim