6/25/2023 0 Comments Samova genodiveSAMOVA_results.ps: this files (eps) can be read with GSview for Windows it contains a map of the sampling points and the barriers between the groups of populations defined by SAMOVA.SAMOVA_finalstructure.arp: an arlequin project file created by appending the input arlequin project file with the genetic structure defined by SAMOVA.SAMOVA.log: this file contains all the steps done by SAMOVA 2.0 and, in case of problems, the location of the problems.SAMOVA_results_arlequin.txt: the genetic structure defined by SAMOVA as well as the fixation indices corresponding to this group structure and their significance level evaluated by 1,000 permutations of populations among groups.It takes time and this time depends on the number of populations you have and the number of simulated annealing processes you wish to perform.Ī set of output files are created by SAMOVA: When the SAMOVA window disappears from your screen that means that the computations are finished. With this option, you can choose between pairwise differences between haplotypes (for DNA data) or sum of squared size differences between haplotypes (for microsatellite data). the type of molecular distance between haplotypes you want to compute (SAMOVA like AMOVA is based on a matrix of distances between haplotypes observed in the whole set of samples).the number of simulated annealing processes you wish to perform (100 seems a good choice).the number K of groups of populations you wish to define (the final structure defined by SAMOVA will contain K groups).the name of the input files (for example: inputdata, in this case, you MUST have in the directory containing the soft the 2 inputfiles used by SAMOVA and these files MUST be called inputdata.geo and inputdata.arp).the name of your population within quotes.an integer number corresponding to the line in the file.Each line must contain five fields separated by a tab character: The geographical input file must be structured the following way. Important notice: SAMOVA 1.0 does not work if two sampling localities have the same geographical coordinates. The file containing the geographic coordinates of the sampling localities of your populations must have the. The order of the populations in the two input files MUST BE THE SAME !!! The Arlequin file must have the SAME NAME as the geographical file with the extension (*.arp). The second one (*.arp) is an Arlequin input file containing the genetic data sampled in your populations. The first one (*.geo) must contain the geographic coordinates of the sampling localities of your populations. The method is described in Dupanloup, Schneider and Excoffier (2002). The method is based on a simulated annealing procedure that aims at maximizing the proportion of total genetic variance due to differences between groups of populations (SAMOVA, Spatial Analysis of MOlecular VAriance). As a by-product, it also leads to the identification of genetic barriers between these groups. SAMOVA 1.0 implements an approach to define groups of populations that are geographically homogeneous and maximally differentiated from each other.
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