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Structurama: Bayesian Inference of Population Structure
Structurama is a program for inferring population structure. Specifically, the program calculates the posterior probability of assigning individuals to different populations. The program takes as input a file containing the allelic information at some number of loci sampled from a collection of indi...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Libertas Academica
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118697/ https://www.ncbi.nlm.nih.gov/pubmed/21698091 http://dx.doi.org/10.4137/EBO.S6761 |
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author | Huelsenbeck, John P. Andolfatto, Peter Huelsenbeck, Edna T. |
author_facet | Huelsenbeck, John P. Andolfatto, Peter Huelsenbeck, Edna T. |
author_sort | Huelsenbeck, John P. |
collection | PubMed |
description | Structurama is a program for inferring population structure. Specifically, the program calculates the posterior probability of assigning individuals to different populations. The program takes as input a file containing the allelic information at some number of loci sampled from a collection of individuals. After reading a data file into computer memory, Structurama uses a Gibbs algorithm to sample assignments of individuals to populations. The program implements four different models: The number of populations can be considered fixed or a random variable with a Dirichlet process prior; moreover, the genotypes of the individuals in the analysis can be considered to come from a single population (no admixture) or as coming from several different populations (admixture). The output is a file of partitions of individuals to populations that were sampled by the Markov chain Monte Carlo algorithm. The partitions are sampled in proportion to their posterior probabilities. The program implements a number of ways to summarize the sampled partitions, including calculation of the ‘mean’ partition—a partition of the individuals to populations that minimizes the squared distance to the sampled partitions. |
format | Online Article Text |
id | pubmed-3118697 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Libertas Academica |
record_format | MEDLINE/PubMed |
spelling | pubmed-31186972011-06-22 Structurama: Bayesian Inference of Population Structure Huelsenbeck, John P. Andolfatto, Peter Huelsenbeck, Edna T. Evol Bioinform Online Short Report Structurama is a program for inferring population structure. Specifically, the program calculates the posterior probability of assigning individuals to different populations. The program takes as input a file containing the allelic information at some number of loci sampled from a collection of individuals. After reading a data file into computer memory, Structurama uses a Gibbs algorithm to sample assignments of individuals to populations. The program implements four different models: The number of populations can be considered fixed or a random variable with a Dirichlet process prior; moreover, the genotypes of the individuals in the analysis can be considered to come from a single population (no admixture) or as coming from several different populations (admixture). The output is a file of partitions of individuals to populations that were sampled by the Markov chain Monte Carlo algorithm. The partitions are sampled in proportion to their posterior probabilities. The program implements a number of ways to summarize the sampled partitions, including calculation of the ‘mean’ partition—a partition of the individuals to populations that minimizes the squared distance to the sampled partitions. Libertas Academica 2011-06-02 /pmc/articles/PMC3118697/ /pubmed/21698091 http://dx.doi.org/10.4137/EBO.S6761 Text en © the author(s), publisher and licensee Libertas Academica Ltd. This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited. |
spellingShingle | Short Report Huelsenbeck, John P. Andolfatto, Peter Huelsenbeck, Edna T. Structurama: Bayesian Inference of Population Structure |
title | Structurama: Bayesian Inference of Population Structure |
title_full | Structurama: Bayesian Inference of Population Structure |
title_fullStr | Structurama: Bayesian Inference of Population Structure |
title_full_unstemmed | Structurama: Bayesian Inference of Population Structure |
title_short | Structurama: Bayesian Inference of Population Structure |
title_sort | structurama: bayesian inference of population structure |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118697/ https://www.ncbi.nlm.nih.gov/pubmed/21698091 http://dx.doi.org/10.4137/EBO.S6761 |
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