Data and scripts for various publications in which our lab was the lead are found below. For data and scripts where members of the lab were co-authors, please contact the corresponding author or check their website. (STILL UNDER CONSTRUCTION)
In general, we have a GitHub repository for the lab (https://github.com/EckertLab), while members also often maintain their own GitHub repositories. Please see the People page for links to individual GitHub repositories.
Publication: Eckert, A. J., P. E. Maloney, D. R. Vogler, C. E. Jensen, A. Delfino Mix, and D. B. Neale. 2015. Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae). Tree Genetics & Genomes 11: 42. doi: 10.1007/s11295-015-0863-0
Processed data: Eckert_et_al_TGG_all_data.xlsx
Raw phenotype data: Eckert_et_all_TGG_raw_phenotype.xlsx
Publication: Friedline, C. J., B. M. Lind, E. M. Hobson, D. E. Harwood, A. D. Mix, P. E. Maloney, and A. J. Eckert. 2015. The genetic architecture of local adaptation I: The genomic landscape of foxtail pine (Pinus balfouriana Grev. & Balf.) as revealed from a high-density linkage map. Tree Genetics & Genomes 11: 49. doi: 10.1007/s11295-015-0866-x
Raw data: PRJNA266319
Genotype data: Friedline_et_al_TGG_File_S2.vcf.tar.gz
Contigs (RADtags): Friedline_et_al_TGG_file_S1.fa
Linkage map: Friedline_et_al_TGG_file_S3.xlsx
Publication: Eckert, A. J., J. D. Liechty, B. R. Tearse, B. Pande and D. B. Neale. 2010. DnaSAM: Software to perform neutrality testing for large datasets with complex null models. Molecular Ecology Resources 10: 542-545. doi: https://doi.org/10.1111/j.1755-0998.2009.02768.x
Archive: DnaSAM
Other notes: The link above takes you to a directory containing the original distribution of DnaSAM, which is a Perl-based program implementing a variety of neutrality tests for complex demographic models based on aligned DNA sequence data. Since its release in 2009, there have been major updates to Perl distributions that are natively installed on most computers, especially Macs. You will need Perl installed on your computer (e.g., version 5.30.2 is what I have currently). On a Mac, you may also need to update/install the Switch and Shell Perl libraries from cpan or elsewhere depending on your operating system and version of Perl. This can be accomplished by:
For Switch:
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Type cpan at a terminal prompt
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At the resulting cpan prompt type: install Switch
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After installation, type exit, which will return you to your terminal
For Shell:
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Type cpan at a terminal prompt
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At the resulting cpan prompt type: install Shell
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After installation, type exit, which will return you to your terminal
You will need the developer tools that are part of Xcode to successfully update/install these Perl libraries. Xcode is available from the Mac app store. If you do not have perl installed at all, please refer to your System Admin folks for help. If you need to figure out what version of Perl is installed, type perl -version at a terminal window or use perl -V for more information. Included in this distribution is a complied version of ms from Richard Hudson. It was complied for a Mac. The source code for ms can be downloaded from: http://home.uchicago.edu/~rhudson1/source/mksamples.html
