Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Mar 1;21(5):589-95.
doi: 10.1093/bioinformatics/bti040. Epub 2004 Sep 23.

Stepwise detection of recombination breakpoints in sequence alignments

Affiliations

Stepwise detection of recombination breakpoints in sequence alignments

Jinko Graham et al. Bioinformatics. .

Abstract

Motivation: We propose a stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints.

Results: We illustrate the approach by analyses of a simulated dataset and alignments of real data from HIV-1 and human chromosome 7. The presented simulation results compare the statistical properties of one-step and two-step procedures. More breakpoints are found with a two-step procedure than with a single application of a given method, particularly for higher recombination rates. At higher recombination rates, the additional breakpoints were located at the cost of only a slight increase in the number of falsely declared breakpoints. However, a large proportion of breakpoints still go undetected.

Availability: A makefile and C source code for phylogenetic profiling and the maximum chi2 method, tested with the gcc compiler on Linux and WindowsXP, are available at http://stat-db.stat.sfu.ca/stepwise/

Contact: jgraham@stat.sfu.ca.

PubMed Disclaimer

Publication types

LinkOut - more resources