MULTIPOP specifications

Information


Unique identifier OMICS_17777
Name MULTIPOP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A set of regions, test statistics obtained for the SNPs in these regions in previous studies of the phenotype (used as priors), and a set of reference data sets from the available populations.
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for MULTIPOP

MULTIPOP in publications

 (6)
PMCID: 5775495
PMID: 29387155
DOI: 10.1111/eva.12527

[…] likely subjected to the crop pollen flow. to assess this, we used a set of rnaseq samples from domesticated and wild native h. annuus (see above) and calculated patterson's d‐statistic using the multipop abbababa2 function in angsd (korneliussen, albrechtsen, & nielsen, ; patterson et al., ). this test uses a four‐member phylogeny and asks whether derived alleles are shared between two […]

PMCID: 5268472
PMID: 28125609
DOI: 10.1371/journal.pone.0170372

[…] the performance of the basic cs algorithm (cs), the proposed modified cs algorithm with pa control (pactrl-cs) and the proposed modified cs algorithm with parameter control and multi-population (multipop-pactrl-cs) by applying them to six classification and two standard time series prediction problems. the classification problems are iris, diabetes diagnoses, thyroid dysfunction, breast […]

PMCID: 4876559
PMID: 27215212
DOI: 10.1186/s13054-016-1330-5

[…] the pc, epcr, and tm genes. we used the resequencing data on these genes available from the seattle snps website (http://snp.gs.washington.edu/seattleseqannotation144/) and selected tag snps using multipop software [] with minimum allele frequency set at 5 % and r2 set at 0.8., snps were genotyped using three commercially available technologies according to the manufacturers’ instructions: […]

PMCID: 4269862
PMID: 25471595
DOI: 10.1186/s12862-014-0254-4

[…] using the afs. while our simulation study is inherently limited by the range of models and sample sizes considered, our results illustrate the promise of afs-based methods like δaδi [], jaatha [], multipop [], and fastsimcoal2 [] for demographic inference and highlight the importance of collecting large population-level genomic samples for analyses of the afs, particularly when interest lies […]

PMCID: 4081578
PMID: 24992022
DOI: 10.1371/journal.pone.0101218

[…] the second component, probapop computes qtl genotype probabilities given marker information at each chromosome location for each family and stores them in xml formatted files. the last component, multipop builds the pooled model using the genotype probabilities, computes fisher tests and estimates the model parameters . the statistical significance of qtls was assessed using the mcqtl test, […]


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MULTIPOP institution(s)
The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel; Molecular Microbiology and Biotechnology Department, Tel-Aviv University, Tel-Aviv, Israel; International Computer Science Institute, Berkeley, CA, USA; Departments of Medicine and Epidemiology and Biostatistics, Institute for Human Genetics and Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, CA, USA
MULTIPOP funding source(s)
Supported by the Israeli Science Foundation, grant no. 04514831, the National Science Foundation, grant IIS-071325412, the National Institutes of Health and the National Cancer Institute, grant R01CA120120, and the Komen Foundation for Breast Cancer Research, grant KG080165.

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