elynx-seq-0.0.1: Handle molecular sequences

Copyright (c) Dominik Schrempf 2017 GPLv3 dominik.schrempf@gmail.com unstable non-portable (not tested) None Haskell2010

ELynx.Simulate.MarkovProcessAlongTree

Description

Calculate transition probability matrices, map rate matrices on trees, populate a tree with states according to a stationary distribution, etc.

The implementation of the Markov process is more than basic and can be improved in a lot of ways.

Synopsis

# Single rate matrix.

simulateNSitesAlongTree :: (PrimMonad m, Measurable a) => Int -> StationaryDistribution -> ExchangeabilityMatrix -> Tree a -> Gen (PrimState m) -> m (Tree [State]) Source #

Simulate a number of sites for a given substitution model. Keep states at internal nodes. The result is a tree with the list of simulated states as node labels.

simulateAndFlattenNSitesAlongTree :: (PrimMonad m, Measurable a) => Int -> StationaryDistribution -> ExchangeabilityMatrix -> Tree a -> Gen (PrimState m) -> m [[State]] Source #

Simulate a number of sites for a given substitution model. Only the states at the leafs are retained. The states at internal nodes are removed. This has a lower memory footprint.

# Mixture models.

simulateNSitesAlongTreeMixtureModel :: (PrimMonad m, Measurable a) => Int -> Vector R -> [StationaryDistribution] -> [ExchangeabilityMatrix] -> Tree a -> Gen (PrimState m) -> m (Tree [State]) Source #

Simulate a number of sites for a given set of substitution models with corresponding weights. Keep states at internal nodes. See also simulateNSitesAlongTree.

simulateAndFlattenNSitesAlongTreeMixtureModel :: (PrimMonad m, Measurable a) => Int -> Vector R -> [StationaryDistribution] -> [ExchangeabilityMatrix] -> Tree a -> Gen (PrimState m) -> m [[State]] Source #

Simulate a number of sites for a given set of substitution models with corresponding weights. Forget states at internal nodes. See also simulateAndFlattenNSitesAlongTree.