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Links

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.
• MaizeGDB recommended papers
• A century of maize literature on Panzea
• Agricultural Biodiversity Blog
• The Archaeobotanist Blog
• James and the giant corn

Maize resources

• Maize Genetics and Genomics Database
• Panzea

• Maize Genome
• ARS-GRIN

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

• libsequence and related software

• BioPerl

• Genetic Analysis Software List

Analysis

Approximate Bayesian Computation

• DIYABC
• popABC
• msABC
• ABCreg etc.

Recombination and Gene Conversion

• Overpaint
• LDHat
• maxdip and maxhap

Simulation

Forward simulation

• Fregene
• SFS Code
• FPG
• EasyPop
• simuPop
• Bottlesim
• rmetasim
• kernelPop
• Nemo and Marlin

Coalescent simulation

• ms and msHot
• MaCS
• SimCoal and a GUI
• Serial-SimCoal
• Genome
• cosi
• treevolve
• FastCoal
• CoaSim
• mlcoalsim
• Splatche

Coalescent with selection

• Innan and Kim
• msms
• mssel

• SelSim

• Thornton and Jensen

Marker-specific simulation

• DAWG sequences with indels
• Seq-Gen sequences
• indel-Seq-Gen sequences with indels
• microsat microsatellites