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      Genome-wide divergence patterns support fine-scaled genetic structuring associated with migration tendency in brown trout

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          CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure.

          Clustering of individuals into populations on the basis of multilocus genotypes is informative in a variety of settings. In population-genetic clustering algorithms, such as BAPS, STRUCTURE and TESS, individual multilocus genotypes are partitioned over a set of clusters, often using unsupervised approaches that involve stochastic simulation. As a result, replicate cluster analyses of the same data may produce several distinct solutions for estimated cluster membership coefficients, even though the same initial conditions were used. Major differences among clustering solutions have two main sources: (1) 'label switching' of clusters across replicates, caused by the arbitrary way in which clusters in an unsupervised analysis are labeled, and (2) 'genuine multimodality,' truly distinct solutions across replicates. To facilitate the interpretation of population-genetic clustering results, we describe three algorithms for aligning multiple replicate analyses of the same data set. We have implemented these algorithms in the computer program CLUMPP (CLUster Matching and Permutation Program). We illustrate the use of CLUMPP by aligning the cluster membership coefficients from 100 replicate cluster analyses of 600 chickens from 20 different breeds. CLUMPP is freely available at http://rosenberglab.bioinformatics.med.umich.edu/clumpp.html.
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            adegenet: a R package for the multivariate analysis of genetic markers.

            The package adegenet for the R software is dedicated to the multivariate analysis of genetic markers. It extends the ade4 package of multivariate methods by implementing formal classes and functions to manipulate and analyse genetic markers. Data can be imported from common population genetics software and exported to other software and R packages. adegenet also implements standard population genetics tools along with more original approaches for spatial genetics and hybridization. Stable version is available from CRAN: http://cran.r-project.org/mirrors.html. Development version is available from adegenet website: http://adegenet.r-forge.r-project.org/. Both versions can be installed directly from R. adegenet is distributed under the GNU General Public Licence (v.2).
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              distruct: a program for the graphical display of population structure

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                Author and article information

                Journal
                Canadian Journal of Fisheries and Aquatic Sciences
                Can. J. Fish. Aquat. Sci.
                Canadian Science Publishing
                0706-652X
                1205-7533
                October 2018
                October 2018
                : 75
                : 10
                : 1680-1692
                Affiliations
                [1 ]Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland.
                [2 ]Department of Biology, University of Turku, FI-20014, Turku, Finland.
                [3 ]Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, P.O. Box 35, Finland.
                [4 ]Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51014 Tartu, Estonia.
                [5 ]Natural Resources Institute Finland, Manamansalontie 90, FI-88300, Paltamo, Finland.
                [6 ]Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland.
                Article
                10.1139/cjfas-2017-0014
                © 2018

                http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining

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