The Nielsen Lab has developed several software packages including:
- ANGSD – Analyses of Next Generation Sequencing Data. Our new program package for analyzing NGS data developed by Thorfinn Korneliusen with help from Anders Albrechtsen and others.
- ngsTools - C/C++ programs to simulate NGS data, to compute estimates of FST, of the sample covariance matrix and of the 2D-SFS. Estimates of population genetics parameters are based on posterior probabilities of genotypes and sample allele frequencies as in Nielsen et al. 2012. Input files can be generated using the ANGSD software.
- ngsF – A program to estimate per-individual inbreeding coefficients
- SweepFinder – can be used to detect the location of a selective sweep based on SNP data. It will also estimate the frequency spectrum of observed SNP data in the presence of missing data
- trueFS – used for finding the ascertainment corrected frequency spectrum based on ascertained SNP data
- codonbias – program will allow the user to estimate selection coefficients relating to optimal codon usage
- CodonRecSim – a program for simulating samples in a codon based models under the coalescent with recombination
- PATRI – (PaTeRnity Inference) a program for paternity analysis of genetic data
- The IM and IMa set of programs for estimating migration rates, divergence times, and effective population sizes were developed in collaboration with Jody Hey’s group.
- MDIV – a program that will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model and under a finite sites model (HKY). For most purposes you probably want to use one of the IM programs instead.
- BAMSE is a phenomenal, and terribly underutilized, program developed by Anders Albrechtsen. It provides a very flexible method for association mapping for multifactorial traits in the presence of gene-gene and gene-environment interactions. I have really no idea why this method is not more used in association mapping studies – but I guess we can’t be too great at advertising.
- Relate – an R package for estimating pair wise relatedness using maximum likelihood for genome-wide data while taking LD into account. This is another program by Anders Albrechtsen.
- MISAT – a program for estimating the likelihood surface for theta (4 times the effective population size times the mutation rate) for population genetic microsatellite data. This program is old. There must be better methods out there.
- MCMC_IBDfinder – an MCMC program by Ida Moltke for estimating posterior probabilities of identity by descent (IBD) sharing between multiple individuals using unphased single nucleotide polymorphism (SNP) data.
- AssotesteR – an R package by Gaston Sanchez with statistical tests and methods for genetic association studies with emphasis on rare variants and binary (dichotomous) traits.
Browse additional programs made available by the Center for Theoretical Evolutionary Genomics here.