HapCUT2: new version of HapCUT that uses a likelihood based model for haplotype assembly and can model trans-errors in Hi-C data

HapCUT a program for haplotype assembly or haplotype phasing using sequence reads from a diploid genome. Source code is available from github

CRISP: program for detection of SNVs and short insertion/deletion variants from high-throughput sequencing of pooled DNA samples. Latest source code is available from github

iAdmix a program to estimate individual admixture proportions from DNA sequencing experiments (exome sequencing, targeted sequencing, low coverage whole-genome sequencing or genotyping). Source code is available from github

Hap-simulator a program for simulating reads for haplotype assembly to evaluate N50 metrics as a function of read length, insert size (paired-end reads), etc

Software that is no longer updated:

AncestryCLL a python program to estimate ancestry likelihoods using genotypes at Ancestry-Informative Markers and HapMap allele frequencies

piCALL a probabilistic method for detection of insertion/deletion polymorphisms (indels) from population-scale sequence data (use CRISP instead of piCALL)

SNIP-Seq one of the first methods designed to leverage sequence data from multiple individuals simultaneously to model site-specific error rates and detect SNPs

HASH implementation of an MCMC algorithm for haplotype assembly from whole-genome sequence data (use HapCUT instead)

LUBOUND program to calculate lower bounds on the minimum number of recombination events in a sample history