Repository for paper looking at phenotypic differences among F1 and F2 oysters from 3 populations in Puget Sound, WA.

starmie: plotting and inference for population structure models 🌟

R-markdown script for geographic population genetic structure analysis with Tess3r

This repository if for creating auto-encoders easily. The main focus of the auto-encoders on this page is for genetic and spectral data analysis but likely could be used for any high dimensional data

Repository for code used in the study "Patterns of population structure and complex haplotype sharing at continental and local scales in field isolates of the green alga Chlamydomonas reinhardtii"

Scripts and notes related to the manuscript: Stuart KC & Cardilini APA 2021 Signatures of selection in a recent invasion reveal adaptive divergence in a highly vagile invasive species. Molecular Ecology 30(6):1419-1434, doi.org/10.1111/mec.15601 † joint first author ‡ joint last author.

In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples.

STRUCTURE and ROLLOFF reimplementations for CS 4775 (Computational Genetics and Genomics)

Interactive interface for pophelper using shiny web framework.

Tutorial for visualising admixture on a map

Scripts for file processing and analysis in phylogenetics and phylogeography

Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files

A data clustering package based on admixture ratios (Q matrix) of population structure analysis.

Quantitative Trait Cluster Association Test in R

rhierbaps: R implementation of hierBAPS

Plague Global Phylogeny Manuscript

Population Structured Bayesian Epistasis Association Mapping

A flexible tool for the multi-resolution localization of causal variants across the genome, accounting for population structure.

vk.com community members sex and age distribution (population pyramid)