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Genotype data for our Veeramah et al. PNAS 2018 paper can be found in a shared google drive folder here


lcMLkin is a C++ program for inferring biological relatedness between pairs of individuals from 2nd generation sequencing data using maximum-likelihood that is particularly effective when read coverage is low. The program is written in collaboration with Rob Patro and is available from the following GitHub link.

aDNA_GenoCaller is a python program that calls genotypes from bam files at positions/regions specified in a bam file while taking into account post mortem damage as estimate by MapDamage and is available from the following GitHub link.

ATLAS (Analysis Tools for Low-coverage and Ancient Samples) is a package that covers all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file. There are sequence data processing tools, diagnostic tools, and variant discovery tools, similar to GATK by the Broad Institute. ATLAS is developed by Vivian Link and Dan Wegmann and is available from the following Bitbucket link.

SBU Genomics

Community website for genomics at Stony Brook

Friends and Collaborators

Michael Hammer, University of Arizona (Primate Genomics and Genetics of Epilepsy)

Joseph Watkins, University of Arizona (Primate Genomics and Genetics of Epilepsy)

Patrick Geary, Institute for Advanced Study (aDNA of Migration Period)

David Caramelli, University of Florence (aDNA of Migration Period)

Guido Barbujani, University of Ferrera (aDNA of Migration Period)

Scott MacEachern, Bowdoin (African Genetic Diversity)

Mark Thomas, UCL (African Genetic Diversity)

Lucia Carbone, OHSU(Primate Genomics)

Omer Gokcumen, Buffalo (Primate Genomics)

Joachim Burger, Mainz (Ancient DNA)

Johannes Krause, Max Planck, Jena (Ancient DNA)

Jeff Kidd, Michigan (Dog Ancient DNA)

Walt Eanes, Stony Brook (Drosophila Evolution)

Mike Bell, Stony Brook (Stickleback Evolution)

Kat Milligan-Myhre, University of Alaska Anchorage (Stickleback Evolution)