Man pages for gehara/PipeMaster
Building and Simulating Coalescent models.
| get.data.structure | Read the observed data to get the simulation parameters; base... |
| get.prior.table | Get a table with prior distributions. |
| get.tree.info | Get tree information |
| H.div | Haplotype Diversity |
| iPyrad.alleles.loci2fasta | iPyrad alleles.loci file to fasta alignments conversion |
| main.menu | Model Builder |
| ms.to.DNAbin | Converts ms output to DNAbin file |
| multiplot | Multiple plot function |
| observed.coexp.sumstat | Observed codemographic hippersummary statistics calculation |
| observed.pw.distances | Observed pairwise distances between tips of tree |
| observed.singlepop.sumstat | Observed summary statistics calculation for single pop... |
| observed.sumstat | Observed summary statistics |
| obs.sumstat.ngs | Observed summary statistics for nexgen data |
| PipeMaster | PipeMaster: A package to build and simulate coalescent models |
| PlotModel | Plot model |
| plotPCs | Principal Component Analysis plot |
| plot.priors | Plot prior distribution |
| plot.sim.obs | Plot simulated data against observed |
| popassign | assignment file example for the Dermatonotus muelleri... |
| PopPlanner | Calls PopPlanner, a java aplication with GUI to build ms... |
| seqs | 200 sequences of the Dermatonotus muelleri frog |
| sim.coaltrees | Simulate coalescent trees using ms |
| sim.coexp | Simulation of codemographic models |
| sim.coexp.ngs | Simulation of codemographic models with ngs data |
| sim.coexpPT | Simulation of codemographic models |
| sim.msABC.sanger | Simulate summary statistics using msABC |
| sim.msABC.sumstat | Simulate summary statistics using msABC |
| sim.ms.sumstat | Simulate summary statistics using ms and PopGenome |
| sim.sp.tree | Simulation of phylogenetic networks under the coalescent |
| single.pop.demog | Simulation of demographic models for single populations. |
| update.priors | Update priors using a prior table |
