frappe protocols

frappe specifications

Information


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

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Documentation


Maintainers


  • person_outline Hua Tang <>
  • person_outline frappe Team <>

Publication for frappe

frappe IN pipelines

 (4)
2016
PMCID: 4839221
PMID: 26823447
DOI: 10.1093/molbev/msw017

[…] same topological structures (supplementary fig. s1, supplementary material online). principle component analysis using eigensoft3.0 (patterson et al. 2006) and population structure analyses using frappe (tang et al. 2005) corroborated these patterns. in particular, the first principal component (variance explained = 16.90%, tracy–widom p = 1.12e-06) separated the outgroup a. cerana […]

2016
PMCID: 4839221
PMID: 26823447
DOI: 10.1093/molbev/msw017

[…] indicated that xinyuan honey bees and a. m. mellifera were separated from the other subspecies (fig. 1c, supplementary fig. s2 and table s6, supplementary material online). clustering analyses with frappe, grouped honey bees from xinyuan and a. m. mellifera into the same cluster if k was less than 5, but with k equal to 5 they were divided into two groups (fig. 1d). our resequenced data support […]

2016
PMCID: 5026255
PMID: 27401233
DOI: 10.1093/molbev/msw129

[…] program in the package eigensoft v5.0 (patterson et al. 2006). the population genetic structure of the native sheep was examined via an expectation maximization algorithm implemented in the program frappe v1.170 (tang et al. 2005). the number of assumed genetic clusters k ranged from 2 to 9, with 10,000 iterations for each run. population genetic differentiation between the three identified […]

2014
PMCID: 4148021
PMID: 25138716
DOI: 10.1186/s12870-014-0225-3

[…] for the 29 sesame strains. the phylogenetic tree was displayed using the software mega5 [44]. was performed using the software eigensoft [45]. the software frappe [46] was used to determine the population structure., additional file 1: additional file 2: , linhai wang and xuelian han contributed equally., competing interests , the authors […]

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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