| Copyright | (c) Dominik Schrempf 2021 |
|---|---|
| License | GPL-3.0-or-later |
| Maintainer | dominik.schrempf@gmail.com |
| Stability | unstable |
| Portability | portable |
| Safe Haskell | None |
| Language | Haskell2010 |
SLynx.Simulate.Options
Description
Creation date: Sun Oct 7 17:29:45 2018.
Available options: -h,--help Show this help text -v,--version Show version -t,--tree-file NAME Specify tree file NAME -s,--substitution-model MODEL Set the phylogenetic substitution model; available models are shown below -m,--mixture-model MODEL Set the phylogenetic mixture model; available models are shown below -l,--length NUMBER Set alignment length to NUMBER -e,--edm-file NAME empirical distribution model file NAME in Phylobayes format -w,--mixture-model-weights [DOUBLE,DOUBLE,...] weights of mixture model components -g,--gamma-rate-heterogeneity (NCAT, SHAPE) number of gamma rate categories and shape parameter -e,--seed [INT] Set seed for the random number generator; list of 32 bit integers with up to 256 elements (default: [0]) -q,--quiet Be quiet -o,--output-file NAME Specify output file NAME
Synopsis
- type GammaRateHeterogeneityParams = (Int, Double)
- data SimulateArguments = SimulateArguments {
- argsTreeFile :: FilePath
- argsSubstitutionModelString :: Maybe String
- argsMixtureModelString :: Maybe String
- argsEDMFile :: Maybe FilePath
- argsSiteprofilesFiles :: Maybe [FilePath]
- argsMixtureWeights :: Maybe [Double]
- argsGammaParams :: Maybe GammaRateHeterogeneityParams
- argsLength :: Int
- argsSeed :: SeedOpt
- simulateArguments :: Parser SimulateArguments
- simulateFooter :: [String]
Documentation
type GammaRateHeterogeneityParams = (Int, Double) Source #
Number of gamma rate categories and alpha parameter.
data SimulateArguments Source #
Arguments needed to simulate sequences.
Constructors
Instances
simulateArguments :: Parser SimulateArguments Source #
Sub command parser.
simulateFooter :: [String] Source #
The model specification is somewhat complicated, so we need to provide additional help.