Software

(all programs written in C)

JADE
documentation
source
example files (.zip)

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.

IM_hypotest
documentation
Dos executable
source

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

migrate_hypotest
documentation
source
(please contact me for distribution)

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

BayCyde
(currently unreleased)

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

This method is now available in BEAST, and see also:
Baele G, Lemey P, Bedford T, Rambaut A, Suchard MA, Alekseyenko AV. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol 2012, 29:2157-2167.
Guy Baele, Wai Lok Sibon Li, Alexei J. Drummond, Marc A. Suchard, Philippe Lemey. Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics Mol Biol Evol (2013) 30(2): 239-243 first published online October 22, 2012 doi:10.1093/molbev/mss243

Hunting Policy
(currently unreleased)

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
(currently unreleased)

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).