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A fast method for the selection of samples in populations with available genealogical data

Hršak, Dalibor; Katanić, Ivan; Ristov, Strahil (2022) A fast method for the selection of samples in populations with available genealogical data. Diversity, 14 (2). ISSN 1424-2818

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Optimal selection of samples in populations should provide the best coverage of sample variations for the available sampling resources. In populations with known genealogical connections, or pedigrees, this amounts to finding the set of samples with the largest sum of mutual distances in a genealogical tree. We present an optimal, and a faster sub-optimal, method for the selection of K samples from a population of N individuals. The optimal method works in time proportional to NK^2, and the sub-optimal in time proportional to NK, which is more practical for large populations. The sub-optimal algorithm can process pedigrees of millions of individuals in a matter of minutes. With the real-life pedigrees, the difference in the quality of the output of the two algorithms is negligible. We provide the Python3 source codes for the two methods.

Item Type: Article
Uncontrolled Keywords: genealogical tree ; sampling plan ; optimal population coverage ; pedigree sampling ; mitochondrial DNA ; Y chromosome
Subjects: TECHNICAL SCIENCES > Computing
TECHNICAL SCIENCES > Basic Technical Sciences
TECHNICAL SCIENCES > Interdisciplinary Technical Sciences
Divisions: Division of Electronics
Project titleProject leaderProject codeProject type
Napredni deterministički i hibridni algoritmi na nizovima, sljedovima i stablima s primjenama u tehničkim znanostima i znanostima o životuRistov, StrahilIP-2018-01-7317HRZZ
Primjena NGS metoda u procjeni genomske varijabilnosti preživačaČubrić Čurik, VlatkaIP-2018-01-8708HRZZ
Napredne metode i tehnologije u znanosti o podatcima i kooperativnim sustavima - IJ za znanost o podatcimaLončarić, SvenKK.
Depositing User: Strahil Ristov
Date Deposited: 24 Mar 2022 11:07
DOI: 10.3390/d14020150

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