Bay Pass Manual 2.1

• Overview
• Before you start
  • How to get BayPass?
  • How to compile BayPass?
  • Input file format
    • The genotyping data file [always required]
    • The pool (haploid) size file [only required for Pool–Seq data]
    • The covariate data file [required for the covariate modes]
    • The covariance matrix file [optional, required for the AUX covariate mode]
• Running BayPass
  • Overview of the different models available in BayPass
    • The core model
    • The standard covariate model and extensions
    • The auxiliary covariate model
  • Detailed overview of all the options
  • Format of the output files
• Miscellaneous R functions
  • The R function simulate.baypass()
    • Description
    • Usage
    • Arguments (in alphabetic order)
    • Values
    • Examples
  • The R function fmd.dist()
    • Description
    • Usage
    • Arguments
    • Values
    • Example
  • The R function geno2YN()
    • Description
    • Usage
    • Arguments
    • Values
    • Example
• Worked Examples
  • Cattle allele count data
    • Analysis under the core model mode: MCMC is run under the core model
    • Analysis under the IS covariate mode: MCMC is run under the core model
    • Analysis under the MCMC covariate mode: MCMC is run under the STD model
    • Analysis under the AUX covariate mode: MCMC is run under the AUX model
  • Littorina Pool–Seq read count data
• Credits
• Copyright
• Contact
• Bibliography
• Appendix Comparisons of the computational efficiency of the different version of BayPass