Software
ARG-Needle
ARG-Needle is an algorithm to reconstruct the genealogical history (ancestral recombination graph, ARG) of large collections of sequenced or genotyped genomes. ARG-Needle-lib is a library that can be used to perform genealogy-wide association and other analyses. This package also implements the ASMC-clust ARG reconstruction algorithm described in the manuscript.
CoalNN
CoalNN is a likelihood-free method, based on convolutional neural networks, for the estimation of TMRCAs and allele ages in sequencing, array, and imputed genomic data.
EpiNN
EpiNN uses a classification algorithm (convolutional neural network) trained with publicly available epigenetic data to recognize genomic regions likely to play a role in the adaptive and innate immune system.
HapNe
HapNe is a method to reconstruct recent past demographic fluctuations in modern and ancient data.
FastSMC
FastSMC is a method to quickly and accurately estimate pairwise identical-by-descent (IBD) regions in the genome. FastSMC estimates the age of IBD segments and scales to large biobank datasets.
ASMC
The Ascertained Sequentially Markovian Coalescent is a method to efficiently estimate pairwise coalescence times along the genome. It can be run using SNP array or whole-genome sequencing (WGS) data.
ARGON
ARGON is a fast simulator of genetic data that samples from the discrete time Wright-Fisher process (DTWF) backwards in time.
IBDmut
IBDmut estimates mutation and non-crossover gene conversion rates using identical-by-descent (IBD) segments shared by distant relatives within a population.
