1. A haplotype estimating apparatus that estimates a haplotype from genotype data including a copy number polymorphism and a nucleotide polymorphism of each individual in a group, comprising a control unit and a storage unit, wherein the storage unit includes: a count number table that stores count numbers obtained by counting polymorphic nucleotides associated with marker sites specified by a label on a copy unit of the copy number polymorphism using the genotype data for each individual, for each type of the polymorphic nucleotides, and the control unit includes: a maximum value-calculating unit that calculates a sum of the count numbers for each of the marker sites based on the count numbers of the individual stored in the count number table to obtain a maximum value of the sum of the count numbers; a polymorphic identification character-enumerating unit that enumerates polymorphic identification characters associated with the type of the polymorphic nucleotides up to the number as many as the count numbers of the polymorphic nucleotides; a character string-creating unit that permutates the enumerated polymorphic identification characters so as to create any character string that has copy units of which the number equals the maximum value; a haplotype character string-storing unit that divides the character string created by the character string-creating unit into two by the copy unit to store the divided strings as a combination of the haplotype character strings; and a haplotype-estimating unit that calculates the number of identical haplotype character strings in the group, obtains a frequency of the haplotype character string in the group, and estimates the combination of the haplotype character strings of each individual of which frequency satisfying a predetermined condition as the combination of the haplotypes.