| [MCMC workshops] |
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Software (all programs written in C) |
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| Jason II annotation database extraction utility. Jason II is a remotely operated submersible operated by Woods Hole Oceanographic Institute. This utility extracts sample collection metadata from the Jason virtual van database and outputs data in Ridge 2000 DMS format. | |
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MCMCthin |
Reads IM surface files (MCMC data) and outputs a thinned MCMC dataset for further analysis using the "cut and paste" R script provided. See the MCMC convergence workshop page for detailed explanations of the functions of the R script. |
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IM_hypotest |
Performs the hypothesis tests described in
Young, Fujio and Vrijenhoek using joint posteriors produced by IM. These
tests have now been incorporated into the distributed version of IM (see
the IM documentation p8). As such, it is probably easiest to view the
output of IM, which does the test automatically. Furthermore, since IM
now implements these tests, I no longer support this software. Please cite: C. R. Young, S. Fujio and R. C. Vrijenhoek. 2008. Directional dispersal between mid-ocean ridges: deep-ocean circulation and gene flow in Ridgeia piscesae. Molecular Ecology, v. 17:7, 1718-1731. doi: 10.1111/j.1365-294X.2008.03609.x |
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migrate_hypotest |
Performs the hypothesis tests described in
Young, Fujio and Vrijenhoek using joint posteriors produced by migrate-n. Please cite: C. R. Young, S. Fujio and R. C. Vrijenhoek. 2008. Directional dispersal between mid-ocean ridges: deep-ocean circulation and gene flow in Ridgeia piscesae. Molecular Ecology, v. 17:7, 1718-1731. doi: 10.1111/j.1365-294X.2008.03609.x |
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BayCyde |
Bayesian cytonuclear disequilibrium: estimates cytonuclear disequilibrium and fits the immigration model as in Young and Draper. |
| JAMN documentation source |
Jason II annotation mosaic navigation extraction utility. This utility extracts navigational metadata from the Jason virtual van database for use in photo mosaic studies. |
| MrAICM documentation source |
Computes AIC analogue from posterior simulations. This program applies the stabilized model discrimination measure AICM to Bayesian phylogenetic analyses. Please cite: Frank J. Stewart, C. R. Young, C. M. Cavanaugh. 2008. Lateral symbiont acquisition in a maternally transmitted chemosynthetic clam endosymbiosis. Molecular Biology and Evolution, v. 25:4, 673-87. doi: 10.1093/molbev/msn010 |
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SPARE |
This program renames sequences input in a fasta file format
based on a name lookup table supplied in a tab delimited text file. The output is also a fasta formatted file. |
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Hunting Policy |
Stage-sex structured population dynamics model in Young and Towbin "Behavioral ecology meets management: effects of infanticide, parental care, and incidentl take on the sustainability of hunted populations" and Caro et al. "Animal breeding systems and big game hunting: models and application." The model allows hunting mortality under three policies (adult male, adult and subsistance hunting) and also includes some incidental take. Mating behavior is addressed in the model, including harem structure, infanticide (mortality-induced and competition-induced), and parental care (both male and female). |
Phoenix |
A software package for microbial population genetics using 454 pyrosequencing. This software identifies sequences by MID tag and locus primer, compresses the data to 100% identical sequences and a table of experimental counts, computes various population genetics summary statistics (pairwise FST, nucleotide and genotype diversities, Tajima’s D family of statistics, etc.), and can be used to create input files for standard population genetics software packages (e.g., LDhat). |
| [MCMC workshops] |