(2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. See Also: read.GeneMapper, write.GenoDive, read.Tetrasat, read.ATetra, read.Structure, read.SPAGeDi, read.POPDIST, read.STRand GenoDive allows for a genotype to be partially missing but polysat does not therefore, if an allele is coded as zero but other alleles are recorded for that sample and locus, the output genotype will just contain the alleles that are present, with the zeros thrown out. If the only alleles listed for a particular individual and locus are zeros, this is interpreted by read.GenoDive as missing data, and Missing(object) (the default, -9) is written in that genotype slot in the genambig object. Each allele must have the same number of digits, although leading zeros can be omitted. Alleles at one locus are concatenated together in one string without any characters to separate them. Separated by tabs are the population number, the clone number (optional), the individual name (used as the sample name in the output) and the genotypes at each locus. The locus names for the genotype object are derived from this line.Įach individual is on one line following the genotype header line. This line contains, separated by tabs, column headers for populations, clones (optional), and individuals, followed by the name of each locus. After that is a header line for the genotype data. The following lines contain the names of populations, which are written to the PopNames slot of the genambig object. On the second line, separated by tabs, are the number of individuals, number of populations, number of loci, maximum ploidy (ignored), and number of digits used to code alleles. The first line of the file is a comment line, which is written to the Description slot of the genambig. read.GenoDive imports data from text files formatted for this program. Details: GenoDive is a Mac-only program for population genetic analysis that allows for polyploid data. The first line of the file is a comment line, which is written to the Description slot of the genambig object. Return Values: A genambig object containing the data from the file. Return Values: A genambig object containing the data from the file.ĭetails: GenoDive is a Mac-only program for population genetic analysis that allows for polyploid data. # create data file (normally done in a text editor or spreadsheet software)Ĭat(c("example comment line", "5\t2\t2\t3\t2", "pop1", "pop2", Install.packages("polysat", repo="", dep=T)
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