Email updates

Keep up to date with the latest news and content from BMC Genetics and BioMed Central.

Open Access Methodology article

Detecting negative selection on recurrent mutations using gene genealogy

Kiyoshi Ezawa12*, Giddy Landan13 and Dan Graur1

Author Affiliations

1 Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA

2 Present address: Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan

3 Present address: Institute of Genomic Microbiology, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf 40225, Germany

For all author emails, please log on.

BMC Genetics 2013, 14:37  doi:10.1186/1471-2156-14-37

Published: 7 May 2013

Additional files

Additional file 1:

Supplementary notes, which consist of Supplementary methods, Supplementary discussion, Tables S1- S16, and Figures S1-S5.

Format: PDF Size: 10.2MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Detailed descriptions of our new parsimony algorithm to enumerate parsimonious mutation scenarios on an incompletely resolved genealogy.

Format: PDF Size: 4.2MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

A ZIP archive that contains the original versions of a Perl module implementing our new parsimony algorithm, as well as of Perl and Bourne shell scripts used for our simulation data analyses to examine the performances of various neutrality tests including our two new tests. It also contains a README file that describes how to use the modules and scripts. (The modules and scripts will run on a Mac OS X terminal. And they should probably run on other UNIX platforms as well, although we have not tested whether they indeed will.) The latest version of the modules and scripts, as well as some null-distributions, can be found in the DENSERM directory at the FTP repository of the Bioinformatics Organization [95].

Format: ZIP Size: 806KB Download file

Open Data