Related Experiment Video
Updated: Mar 7, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification
Zachary A Szpiech1, Alexandra Blant2, Trevor J Pemberton2
1Department of Bioengineering and Therapeutic Sciences, University of California - San Francisco, San Francisco, CA 94158, USA.
Summary:
Runs of homozygosity (ROH) are important genomic features that manifest when identical-by-descent haplotypes are inherited from parents. Their length distributions and genomic locations are informative about population history and they are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. Here, we present software implementing a model-based method ( Pemberton et al., 2012 ) for inferring ROH in genome-wide SNP datasets that incorporates population-specific parameters and a genotyping error rate as well as provides a length-based classification module to identify biologically interesting classes of ROH. Using simulations, we evaluate the performance of this method.
Availability And Implementation:
GARLIC is written in C ++. Source code and pre-compiled binaries (Windows, OSX and Linux) are hosted on GitHub ( https://github.com/szpiech/garlic ) under the GNU General Public License version 3.
Contact:
zachary.szpiech@ucsf.edu.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
More Related Videos
Related Concept Videos
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Modern Molecular Taxonomy
Evolutionary Relationships through Genome Comparisons
Genomics
Applications of Molecular Taxonomy
Gene Duplication and Divergence
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...

