Computer Code Disclaimer

Below you will find links to various pieces of computer code, mostly R scripts, used by myself and other members of the lab. When applicable the links are grouped by publication. We have made every effort to comment our code, but these are distributed as is and are not intended to act as stand alone programs. You are free to download and modify them as needed. If you find them useful and happen to be in the neighborhood or run into one of us at a conference, please note that we will only accept payments in the form of beer.

Friday, October 28, 2011

Species tree - gene tree discordance for the Balfourianae

The purpose of this script is to perform a two stage bootstrap of loci and sites within loci for a set of 191 nuclear genes being used to infer the species tree for Pinus subsection Balfourianae. The actual bootstrap takes a long time to run. Note that this is used in the context of summary statistic based methods for species tree inference - MDC, STAR and STEAC. Per locus gene trees are inferred from average (across samples) pairwise distances under the Kimura (1980) model of DNA sequence evolution which were analyzed using the neighbor joining algorithm.

The R script is here: bootstrap

Note that you will have to load the appropriate R libraries, change the paths to the infiles, make sure to comment out things that you do not want to run, and "uncomment" out things that you do want to run to make it work for you. It also assumes that the following R scripts have been run successfully: (1) data generation, (2) analysis, and (3) pairwise inference.

Author: Andrew J. Eckert

Thursday, October 27, 2011

DnaSAM - DNA Sequence Analysis and Manipulation

DnaSAM is a Perl program that assists in high-throughout estimation of diversity and divergence from DNA sequence alignments. It was written by John Liechty (Department of Plant Sciences, University of California at Davis) with population genetic input from A. J. Eckert. 

It is available here, and if you use DnaSAM please cite the following 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.