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frappe specifications


Unique identifier OMICS_02076
Name frappe
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Input data Either two or three files: Parameter file, Genotype file, Individual file.
Output data The ancestry proportion estimates for each individual.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes


No version available


  • person_outline Hua Tang
  • person_outline frappe Team

Publication for frappe

frappe citations


Nonparametric approaches for population structure analysis

Hum Genomics
PMCID: 5944014
PMID: 29743099
DOI: 10.1186/s40246-018-0156-4

[…] populations. Similar to STRUCTURE, PARTITION [], BAPS/BAPS2 [, ], and GENELAND [] take the same modeling approach, which is based on an MCMC algorithm, to sample the posterior distribution. Moreover, FRAPPE [] and ADMIXTURE [, ] adopt the same modeling approach but rely on maximizing the likelihood using an expectation-maximization (EM) algorithm instead of sampling the posterior distribution. In […]


Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater

Nat Commun
PMCID: 5893588
PMID: 29636446
DOI: 10.1038/s41467-018-03722-x
call_split See protocol

[…] r PCA analyses and phylogeny reconstruction. Population structure was inferred by ADMIXTURE with tenfold cross-validation. The ancestral sequences of finless porpoises were inferred using the program frappe without assuming any prior information about their structure. Identical-by-descent (IBD) haplotypes was estimated using BEAGLE and linkage disequilibrium (LD) pattern and the coefficient of det […]


Whole genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi feralization

PMCID: 5905515
PMID: 29668959
DOI: 10.1093/gigascience/giy019

[…] al alleles for each SNP. Only biallelic autosomal SNPs were used to calculate the distance matrix. PCA was performed using EIGENSOFT, version 6.0.1 [, ], and population structures were inferred using FRAPPE software, version 1.1 []. Both the PCA and population structures were calculated based on autosomal SNPs after removing highly correlated SNP pairs using PLINK, version 1.07 (PLINK, RRID:SCR_00 […]


Whole genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants

3 Biotech
PMCID: 5801106
PMID: 29430376
DOI: 10.1007/s13205-018-1140-3

[…] We estimated the population structure using FRAPPE on the 172,922 SNPs. We analyzed ancestry by increasing the number of clusters, K, from 2 to 6. At K = 2, the non-anthocyanin accessions were not distinctly separated from the high-anthocyanin […]


Type 2 Diabetes Genetic Risk Scores Are Associated With Increased Type 2 Diabetes Risk Among African Americans by Cardiometabolic Status

PMCID: 5757425
PMID: 29326538
DOI: 10.1177/1179551417748942
call_split See protocol

[…] To control for potential confounding due to admixture in African Americans, 47 ancestry informative markers (AIMs) common across all 4 studies were used to determine individual admixture using Frappe (version 1.1) in a 2-population model., These AIMs were chosen based on their availability on Affymetrix 6.0 platform in addition to their ability to maximize European and African allele freque […]


Evaluating genetic ancestry and self reported ethnicity in the context of carrier screening

BMC Genet
PMCID: 5704547
PMID: 29179688
DOI: 10.1186/s12863-017-0570-y
call_split See protocol

[…] In order to estimate the genetic ancestry of our samples, we modified the Expectation Maximization (EM) Algorithm used in FRAPPE [, ]. We assumed a paradigm where an individual’s genome is divided into segments of different ancestral origin from a set of geographic regions. Our goal was to estimate the proportion of ance […]


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frappe institution(s)
Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Statistics, Stanford University, Stanford, CA, USA; Department of Genetics, Stanford University, Stanford, CA, USA; Division of Research, Kaiser Permanente, Oakland, CA, USA
frappe funding source(s)
Supported in part by a Stanford Graduate Fellowship.

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