The program begins by finding maximum likelihood estimates of the recombination fractions (for the specified locus order); these are then used to find, for each pedigree in the data set, the particular phase choice having the highest likelihood< for that pedigree. (The algorithm used for this purpose is described in [ Green (1988) ]. For each individual with parents in the pedigree, the chromosomes are displayed (maternal first, then paternal). (The individual's ID # appears to the left of the maternal chromosome.) A '0' (resp. '1') means the allele is of known phase and is of grandmaternal (resp. grandpaternal) origin. For alleles of unknown phase, 'o' and 'i' are used instead, denoting the grandparental origin in the most likely phase choice. '-' means that the locus is noninformative.
To the right of the chromosome appears the number of recombinations. Beneath the chromosome appear the names of any informative loci which are out of phase with the nearest informative loci on either side; when the loci are closely spaced, these are candidate data errors. Following the chromosome pictures for all the families is a list of recombinant chromosomes. For each pair of loci, the chromosomes are listed in which there is a recombination between those two loci (and no intervening locus is informative). The recombinant chromosomes are designated by family number, individual ID #, and M or P (for maternal or paternal). Following the list of recombinant chromosomes is a list of groups of loci not separated by any crossovers in the data set; and finally, the maximum likelihood recombination fractions which were used in computing probabilities of the phase choices.
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