Species tree - gene tree discordance for the Balfourianae

2011-10-28T08:45:00.000-07:00

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

DnaSAM - DNA Sequence Analysis and Manipulation

2011-10-27T07:52:00.000-07:00

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.

(Un)Useful Computer Code

Species tree - gene tree discordance for the Balfourianae

DnaSAM - DNA Sequence Analysis and Manipulation