SweepFinder2: Increased sensitivity, robustness and flexibility

Michael Degiorgio; Christian D. Huber; Melissa J. Hubisz; Ines Hellmann; Rasmus Nielsen

doi:10.1093/bioinformatics/btw051

SweepFinder2: Increased sensitivity, robustness and flexibility

Michael Degiorgio, Christian D. Huber, Melissa J. Hubisz, Ines Hellmann, Rasmus Nielsen

Research output: Contribution to journal › Article › peer-review

141 Scopus citations

Abstract

SweepFinder is a widely used program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection. Moreover, SweepFinder2 has increased flexibility that enables the user to specify test sites, set the distance between test sites and utilize a recombination map.

Original language	English (US)
Pages (from-to)	1895-1897
Number of pages	3
Journal	Bioinformatics
Volume	32
Issue number	12
DOIs	https://doi.org/10.1093/bioinformatics/btw051
State	Published - Jun 15 2016

All Science Journal Classification (ASJC) codes

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

Access to Document

10.1093/bioinformatics/btw051

Cite this

@article{ba2a1c5ef24e4f6db5604d53b777c560,

title = "SweepFinder2: Increased sensitivity, robustness and flexibility",

abstract = "SweepFinder is a widely used program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection. Moreover, SweepFinder2 has increased flexibility that enables the user to specify test sites, set the distance between test sites and utilize a recombination map.",

author = "Michael Degiorgio and Huber, {Christian D.} and Hubisz, {Melissa J.} and Ines Hellmann and Rasmus Nielsen",

note = "Publisher Copyright: {\textcopyright} 2016 The Author 2016.",

year = "2016",

month = jun,

day = "15",

doi = "10.1093/bioinformatics/btw051",

language = "English (US)",

volume = "32",

pages = "1895--1897",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "12",

}

TY - JOUR

T1 - SweepFinder2

T2 - Increased sensitivity, robustness and flexibility

AU - Degiorgio, Michael

AU - Huber, Christian D.

AU - Hubisz, Melissa J.

AU - Hellmann, Ines

AU - Nielsen, Rasmus

PY - 2016/6/15

Y1 - 2016/6/15

N2 - SweepFinder is a widely used program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection. Moreover, SweepFinder2 has increased flexibility that enables the user to specify test sites, set the distance between test sites and utilize a recombination map.

AB - SweepFinder is a widely used program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection. Moreover, SweepFinder2 has increased flexibility that enables the user to specify test sites, set the distance between test sites and utilize a recombination map.

UR - http://www.scopus.com/inward/record.url?scp=84976498979&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84976498979&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btw051

DO - 10.1093/bioinformatics/btw051

M3 - Article

C2 - 27153702

AN - SCOPUS:84976498979

SN - 1367-4803

VL - 32

SP - 1895

EP - 1897

JO - Bioinformatics

JF - Bioinformatics

IS - 12

ER -

SweepFinder2: Increased sensitivity, robustness and flexibility

Abstract

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this