aspartik.b3.likelihoods

Felsenstein's tree likelihood calculators.

class Likelihood:▶View source

class Likelihood(Stateful, Protocol):
    """
    Tree likelihood calculator

    This object calculates the likelihood of a tree given the sequence data
    using Felsenstein's tree pruning algorithm.

    There are several implementations, each with its own options.
    """

    def propose(self) -> None:
        """
        Fetches the current model state and starts the calculations.

        Each implementations are responsible for pulling the state.

        Depending on the implementation, `propose` might start the calculation
        in parallel and return.  In this case `likelihood` will block on it.
        """
        ...

    def likelihood(self) -> float:
        """
        Returns the tree likelihood calculated.

        If `propose` was called during this epoch, this must the likelihood as
        a result of the proposal.  If `accept` or `reject` was called last,
        this method must return the last accepted likelihood.
        """
        ...

    def num_patterns(self) -> int:
        """Number of unique state patterns in the underlying alignment"""
        ...

Tree likelihood calculator

This object calculates the likelihood of a tree given the sequence data using Felsenstein's tree pruning algorithm.

There are several implementations, each with its own options.

def propose(self) -> None

▶View source

    def propose(self) -> None:
        """
        Fetches the current model state and starts the calculations.

        Each implementations are responsible for pulling the state.

        Depending on the implementation, `propose` might start the calculation
        in parallel and return.  In this case `likelihood` will block on it.
        """
        ...

Fetches the current model state and starts the calculations.

Each implementations are responsible for pulling the state.

Depending on the implementation, propose might start the calculation in parallel and return. In this case likelihood will block on it.

def likelihood(self) -> float

▶View source

    def likelihood(self) -> float:
        """
        Returns the tree likelihood calculated.

        If `propose` was called during this epoch, this must the likelihood as
        a result of the proposal.  If `accept` or `reject` was called last,
        this method must return the last accepted likelihood.
        """
        ...

Returns the tree likelihood calculated.

If propose was called during this epoch, this must the likelihood as a result of the proposal. If accept or reject was called last, this method must return the last accepted likelihood.

def num_patterns(self) -> int

▶View source

    def num_patterns(self) -> int:
        """Number of unique state patterns in the underlying alignment"""
        ...

Number of unique state patterns in the underlying alignment

def accept(self) -> None

▶View source

    def accept(self) -> None:
        """Accept changes made during the current step"""

Accept changes made during the current step

def reject(self) -> None

▶View source

    def reject(self) -> None:
        """Reject changes made during the current step

        This method must roll the state of the object back to how it was at the
        beginning of the MCMC step.
        """

Reject changes made during the current step

This method must roll the state of the object back to how it was at the beginning of the MCMC step.

class CPU4Likelihood:

4-state DNA likelihood calculator.

It's synchronous. CUDALikelihood should be used for parallel calculations for alignments larger than 100Kb.

def likelihood(self, /)