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Metapop specifications

Information


Unique identifier OMICS_32679
Name Metapop
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jean-Paul Soularue

Publication for Metapop

Metapop citations

 (18)
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Using population viability analysis, genomics, and habitat suitability to forecast future population patterns of Little Owl Athene noctua across Europe

2017
Ecol Evol
PMCID: 5743613
PMID: 29299275
DOI: 10.1002/ece3.3629
call_split See protocol

[…] Using the population viability software RAMAS/GIS and RAMAS Metapop (Akçakaya & Root, ), a PVA was conducted on the Little Owl on a continent scale with the aim of evaluating the population trend and the future distribution of the species in different European […]

library_books

A Unified Characterization of Population Structure and Relatedness

2017
Genetics
PMCID: 5560808
PMID: 28550018
DOI: 10.1534/genetics.116.198424

[…] s to evaluate the performance of our FST estimates, and we looked at 1000 Genomes SNP data to explore the role of rare variants on the estimates. Some of the simulations were conducted with sim.genot.metapop.t available in the hierfstat package (). The migration model we used allows for a matrix of migration rates between each pair of populations, and the mutation model allows for multiple alleles […]

library_books

Phylogeography and Conservation Genetics of the Ibero Balearic Three Spined Stickleback (Gasterosteus aculeatus)

2017
PLoS One
PMCID: 5261773
PMID: 28118391
DOI: 10.1371/journal.pone.0170685

[…] ns can be predicted from the contribution of each of them to the overall species level allelic diversity [, ]. Such a contribution was calculated for both the nuclear and mitochondrial datasets using METAPOP 2.0.a1 []. We ran the Population Analysis implemented in METAPOP applying rarefaction to correct for sample size and using N to determine the weight given to each subpopulation when calculatin […]

library_books

Hemizygosity Enhances Purifying Selection: Lack of Fast Z Evolution in Two Satyrine Butterflies

2016
Genome Biol Evol
PMCID: 5174731
PMID: 27590089
DOI: 10.1093/gbe/evw214

[…] ius melpomene (). Sequences that hit the same gene in M. cinxia but distinct genes in H. melpomene were excluded.Z-linked/autosomal annotations of genes in M. cinxia (, http://www.helsinki.fi/science/metapop/research/mcgenome2_downloads.html; last accessed February 2015) were propagated to their predicted orthologs in M. jurtina and P. tithonus. We removed ORFs predicted to be Z-linked based on M. […]

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Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

2016
PMCID: 4777131
PMID: 26772750
DOI: 10.1534/g3.115.023655

[…] were identified by running HaploMerger on a merge of Hmel2, and the M. cinxia version 1 genome superscaffolds (Melitaea_cinxia_superscaffolds_v1.fsa.gz, downloaded from http://www.helsinki.fi/science/metapop/research/mcgenome2_downloads.html on July 14, 2015). Overlaps (nodes) detected by HaploMerger between Hmel2 scaffolds and M. cinxia superscaffolds were used to confirm synteny based on known c […]

library_books

Advances in global sensitivity analyses of demographic based species distribution models to address uncertainties in dynamic landscapes

2016
PeerJ
PMCID: 4958004
PMID: 27547529
DOI: 10.7717/peerj.2204

[…] e., habitat patches) using a raster-based habitat suitability map of a 420.3 km2 region in the park. This population map provides the basis on which metapopulation dynamics are simulated in the RAMAS Metapop module. A total of 46 populations were identified by the RAMAS patch detection algorithm, which was consistent with the actual distribution of trees (, ). The authors used aerial photography t […]

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Metapop institution(s)
BIOGECO, INRA, Univ. Bordeaux, Cestas, France; INRA - UMR1347 Agroécologie, Dijon, France
Metapop funding source(s)
Supported by the European Research Council through the Advanced Grant Project TREEPEACE (#FP7-339728), and by the French National Research Agency (ANR) in the frame of the Investments for the future Programme, within the Cluster of Excellence COTE (ANR-10-LABX45), and through the research project ANR MeCC (ANR-13-ADAP-006_02).

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