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abc_timeadapt

TimeAdapt makes a joint inference of demography and selection from longitudinal population genomic data. The inference is based on approximate Bayesian computation via random forest. It takes whole genome data and information about the ages of samples to perform simulations (using SLiM + pyslim/msprime).

abcquinoa

Scripts in R for an an approximate Bayesian computation analysis of ancient Quinoa gene pools and their contribution to modern varieties in Antofagasta

abcrftutorial

Crash Course on Approximate Bayesian Computation in Population Genetics

abcsaxicola

blue-caterpillar

Programme to perform individual population assignment based on linked microsatellite data

dar_abc

Analysis of the Dated Archaeological Record with Approximate Bayesian Computation

diyabcskylineplot

DIYABCskylineplot: A suite of R scripts to perform a Approximate Bayesian Computation Skyline Plot

drifttest

DriftTest is a computer program whose purpose is to is to detect loci under selection based on changes in allele frequencies between two time samples of the same population.

drifttest-evaluation

Evaluation of the detection of locus under selection with temporal Fst outliers with the program drifttest

lmse

Program to obtain maximum likelihood estimates of demographic parameters theta0, theta1 & tau of a stepwise demographic expansion from haplotypic data of linked microsatellite loci.

manuscript-tracking-selection

manuscript material for the Tracking-selection paper

microsatabc-im

A script in R to perform an Random Forest Approximate Bayesian Computation analysis under the Isolation with Migration model from microsatellite data

mnavascues

Config files for my GitHub profile.

siplusa

Population genetics forward simulation with self-incompatibility system and partial asexuality

slim

SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.

tracking-selection

Pipeline to simulate, calculate and prepare the reference table for ABC-RF analysis.