On the minimum number of topologies explaining a sample of DNA sequences

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On the minimum number of topologies explaining a sample of DNA sequences. / Wiuf, Carsten.

I: Theoretical Population Biology, Bind 62, Nr. 4, 01.12.2002, s. 357-363.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Wiuf, C 2002, 'On the minimum number of topologies explaining a sample of DNA sequences', Theoretical Population Biology, bind 62, nr. 4, s. 357-363. https://doi.org/10.1016/S0040-5809(02)00004-7

APA

Wiuf, C. (2002). On the minimum number of topologies explaining a sample of DNA sequences. Theoretical Population Biology, 62(4), 357-363. https://doi.org/10.1016/S0040-5809(02)00004-7

Vancouver

Wiuf C. On the minimum number of topologies explaining a sample of DNA sequences. Theoretical Population Biology. 2002 dec. 1;62(4):357-363. https://doi.org/10.1016/S0040-5809(02)00004-7

Author

Wiuf, Carsten. / On the minimum number of topologies explaining a sample of DNA sequences. I: Theoretical Population Biology. 2002 ; Bind 62, Nr. 4. s. 357-363.

Bibtex

@article{f179ed0706df4d40a02eb655b37288b1,
title = "On the minimum number of topologies explaining a sample of DNA sequences",
abstract = "In this article I derive an alternative algorithm to Hudson and Kaplan's (Genetics 111, 147-165) algorithm that gives a lower bound to the number of recombination events in a sample's history. It is shown that the number, T M, found by the algorithm is the least number of topologies required to explain a set of DNA sequences sampled under the infinite-site assumption. Let T=(T1,⋯,Tr) be a list of topologies compatible with the sequences, i.e., Tk is compatible with an interval, I k, of sites in the alignment. A characterization of all lists having TM topologies is given and it is shown that TM relates to specific patterns in the alignment, here called chain series. Further, a number of theorems relating general lists of topologies to the number TM is presented. The results are discussed in relation to the true minimum number of recombination events required to explain an alignment.",
keywords = "Algorithm, Recombination, SNP, Topology",
author = "Carsten Wiuf",
year = "2002",
month = dec,
day = "1",
doi = "10.1016/S0040-5809(02)00004-7",
language = "English",
volume = "62",
pages = "357--363",
journal = "Theoretical Population Biology",
issn = "0040-5809",
publisher = "Academic Press",
number = "4",

}

RIS

TY - JOUR

T1 - On the minimum number of topologies explaining a sample of DNA sequences

AU - Wiuf, Carsten

PY - 2002/12/1

Y1 - 2002/12/1

N2 - In this article I derive an alternative algorithm to Hudson and Kaplan's (Genetics 111, 147-165) algorithm that gives a lower bound to the number of recombination events in a sample's history. It is shown that the number, T M, found by the algorithm is the least number of topologies required to explain a set of DNA sequences sampled under the infinite-site assumption. Let T=(T1,⋯,Tr) be a list of topologies compatible with the sequences, i.e., Tk is compatible with an interval, I k, of sites in the alignment. A characterization of all lists having TM topologies is given and it is shown that TM relates to specific patterns in the alignment, here called chain series. Further, a number of theorems relating general lists of topologies to the number TM is presented. The results are discussed in relation to the true minimum number of recombination events required to explain an alignment.

AB - In this article I derive an alternative algorithm to Hudson and Kaplan's (Genetics 111, 147-165) algorithm that gives a lower bound to the number of recombination events in a sample's history. It is shown that the number, T M, found by the algorithm is the least number of topologies required to explain a set of DNA sequences sampled under the infinite-site assumption. Let T=(T1,⋯,Tr) be a list of topologies compatible with the sequences, i.e., Tk is compatible with an interval, I k, of sites in the alignment. A characterization of all lists having TM topologies is given and it is shown that TM relates to specific patterns in the alignment, here called chain series. Further, a number of theorems relating general lists of topologies to the number TM is presented. The results are discussed in relation to the true minimum number of recombination events required to explain an alignment.

KW - Algorithm

KW - Recombination

KW - SNP

KW - Topology

UR - http://www.scopus.com/inward/record.url?scp=0036885956&partnerID=8YFLogxK

U2 - 10.1016/S0040-5809(02)00004-7

DO - 10.1016/S0040-5809(02)00004-7

M3 - Journal article

C2 - 12427459

AN - SCOPUS:0036885956

VL - 62

SP - 357

EP - 363

JO - Theoretical Population Biology

JF - Theoretical Population Biology

SN - 0040-5809

IS - 4

ER -

ID: 203903433