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2019-05-22-oxford

Oxford Software Carpentry Workshop

alleletraj

ancestralpaths

AncestralPaths is a local ancestry painting technique based on genealogies produced by RELATE. The method aims to assign 'path' ancestries to segments of chromosomes the decribe the path back through a population history that segment has taken.

ccr5_paper

Source code from the paper: "Tracing the evolutionary path of the CCR5delta32 deletion via ancient and modern genomes" (2023) medRxiv

chicken_paper

Source code from the paper: "The biocultural origins and dispersal of domestic chickens" (2022) PNAS

clues

Coalescent Likelihood Under Effects of Selection - Inferring selection & allele frequency trajectories from nucleotide data

ctvt_paper

Source code from the paper: "The evolutionary history of dogs in the Americas" (2018) Science

mesoneo_paper

Source code from the paper: "The Selection Landscape and Genetic Legacy of Ancient Eurasians" (2022) bioRxiv

ms_paper

Source code from the paper: "Elevated Genetic Risk for Multiple Sclerosis Originated in Steppe Pastoralist Populations." (2022) bioRxiv

palm

Polygenic Adaptation Likelihood Method - Inferring natural selection on complex traits from whole-genome genealogies

planets

SWC Workshop Git Lesson

qpbrute

Heuristic search algorithm for fitting qpGraph models

rabbit_paper

Source code from the paper: "Rabbits and the Specious Origins of Domestication" (2018) TREE

refpanel

Pipeline to build a large human reference panel, using publicly available genomes

selection

sulawesi_paper

Source code from the paper: "Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events" (2018) Proc. R. Soc. B

temporal-selection

Temporal selection exercises for PopGen21