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
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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