Simulate.Options

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

Documentation

type GammaRateHeterogeneityParams = (Int, Double)

Number of gamma rate categories and alpha parameter.

data SimulateArguments

Arguments needed to simulate sequences.

Constructors

SimulateArguments

Fields

• argsTreeFile :: FilePath
• argsSubstitutionModelString :: Maybe String
• argsMixtureModelString :: Maybe String
• argsEDMFile :: Maybe FilePath
• argsSiteprofilesFiles :: Maybe [FilePath]
• argsMixtureWeights :: Maybe [Double]
• argsGammaParams :: Maybe GammaRateHeterogeneityParams
• argsLength :: Int
• argsMaybeSeed :: Maybe [Word32]

type Simulate = LoggingT (ReaderT SimulateArguments IO)

A simulation can log stuff and read the necessary arguments.

simulateArguments :: Parser SimulateArguments

Sub command parser.

simulateFooter :: String

The model specification is somewhat complicated, so we need to provide additional help.