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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 citations

 (6)
library_books

Gene flow in Argentinian sunflowers as revealed by genotyping‐by‐sequencing data

2017
Evol Appl
PMCID: 5775495
PMID: 29387155
DOI: 10.1111/eva.12527

[…] were 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 member […]

library_books

Master Leader Slave Cuckoo Search with Parameter Control for ANN Optimization and Its Real World Application to Water Quality Prediction

2017
PLoS One
PMCID: 5268472
PMID: 28125609
DOI: 10.1371/journal.pone.0170372

[…] There are plentiful studies on the ANN, particularly in relation to its application to classification problems. Therefore, we compared Multipop-PaCtrl-CS as the best method among those examined in the previous section with the most recent methods in the literature that are mainly related to our proposed method and that employed the s […]

call_split

Association of common genetic variation in the protein C pathway genes with clinical outcomes in acute respiratory distress syndrome

2016
PMCID: 4876559
PMID: 27215212
DOI: 10.1186/s13054-016-1330-5
call_split See protocol

[…] in 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: Illumi […]

library_books

Sampling strategies for frequency spectrum based population genomic inference

2014
BMC Evol Biol
PMCID: 4269862
PMID: 25471595
DOI: 10.1186/s12862-014-0254-4

[…] ed 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 in […]

call_split

Genetic Control of Water Use Efficiency and Leaf Carbon Isotope Discrimination in Sunflower (Helianthus annuus L.) Subjected to Two Drought Scenarios

2014
PLoS One
PMCID: 4081578
PMID: 24992022
DOI: 10.1371/journal.pone.0101218
call_split See protocol

[…] es. 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, wh […]

call_split

Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out of Africa Expansion

2012
Genetics
PMCID: 3454885
PMID: 22865734
DOI: 10.1534/genetics.112.141846
call_split See protocol

[…] the scenarios that involved three populations and 50 chromosomes in the scenarios that involved two populations. For each demographic scenario, we computed the AFS with our polynomial-based approach (MultiPop) and with the finite-difference method (∂a∂i) and compared each AFS with the AFS computed with Monte Carlo simulations. The different models and parameters used in the simulations are describ […]

Citations

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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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