UC Davis Links
- UC Davis Genome Center
- CAES Core
- Plant Sciences Biocomputing Center
- Genetics Graduate Group
- Plant Biology Graduate Group
- Hort & Agronomy Graduate Group
- UC Davis Plant Breeding
Good Reading
- R.E.H.A.B.
- EvolFri reading group
- Morrell Lab journal club
- MaizeGDB recommended papers
- A century of maize literature on Panzea
- Agricultural Biodiversity Blog
- The Archaeobotanist Blog
- James and the giant corn
Maize resources
Software
A smattering of popgen software packages. If you know of one that is not listed, or a link is broken, please contact me.
General Popgen
Analysis
Approximate Bayesian Computation
Recombination and Gene Conversion
Simulation
Forward simulation
Coalescent simulation
- ms and msHot
- MaCS
- SimCoal and a GUI
- Serial-SimCoal
- Genome
- cosi
- treevolve
- FastCoal
- CoaSim
- mlcoalsim
- COMPASS
- Splatche
Coalescent with selection
Marker-specific simulation
- DAWG sequences with indels
- Seq-Gen sequences
- indel-Seq-Gen sequences with indels
- microsat microsatellites