elynx-markov-0.6.0.0: Simulate molecular sequences along trees
Copyright(c) Dominik Schrempf 2021
LicenseGPL-3.0-or-later
Maintainerdominik.schrempf@gmail.com
Stabilityunstable
Portabilityportable
Safe HaskellNone
LanguageHaskell2010

ELynx.Data.MarkovProcess.AminoAcid

Description

Creation date: Tue Jan 29 09:29:19 2019.

The order of amino acids is alphabetic.

Synopsis

Amino acid substitution models

lg :: SubstitutionModel Source #

LG substitution model.

lgCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel Source #

LG substitution model with maybe a name and a custom stationary distribution.

wag :: SubstitutionModel Source #

LG substitution model.

wagCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel Source #

LG substitution model with maybe a name and a custom stationary distribution.

poisson :: SubstitutionModel Source #

Poisson substitution model.

poissonCustom :: Maybe String -> StationaryDistribution -> SubstitutionModel Source #

Poisson substitution model with maybe a name and a custom stationary distribution.

gtr20 :: [Double] -> StationaryDistribution -> SubstitutionModel Source #

General time reversible (GTR) substitution model for amino acids.

Convenience functions

alphaToPamlVec :: Vector R -> Vector R Source #

Convert an amino acid vector in alphabetical order to a vector in PAML order.

pamlToAlphaVec :: Vector R -> Vector R Source #

Convert an amino acid vector in PAML order to a vector in alphabetical order.