# API reference

Full auto-generated API documentation for all public classes and functions.

## Sampler

```{eval-rst}
.. automodule:: pysinger.sampler
   :members:
   :undoc-members:
```

## Data structures

```{eval-rst}
.. automodule:: pysinger.data.node
   :members:
   :undoc-members:

.. automodule:: pysinger.data.branch
   :members:
   :undoc-members:

.. automodule:: pysinger.data.tree
   :members:
   :undoc-members:

.. automodule:: pysinger.data.recombination
   :members:
   :undoc-members:

.. automodule:: pysinger.data.interval
   :members:
   :undoc-members:

.. automodule:: pysinger.data.arg
   :members:
   :undoc-members:
```

## HMM

```{eval-rst}
.. automodule:: pysinger.hmm.coalescent
   :members:
   :undoc-members:

.. automodule:: pysinger.hmm.emission
   :members:
   :undoc-members:

.. automodule:: pysinger.hmm.bsp
   :members:
   :undoc-members:

.. automodule:: pysinger.hmm.tsp
   :members:
   :undoc-members:
```

## MCMC

```{eval-rst}
.. automodule:: pysinger.mcmc.threader
   :members:
   :undoc-members:
```

## I/O

```{eval-rst}
.. automodule:: pysinger.io.vcf_reader
   :members:
   :undoc-members:

.. automodule:: pysinger.io.tskit_writer
   :members:
   :undoc-members:
```

## Rates

```{eval-rst}
.. automodule:: pysinger.rates.rate_map
   :members:
   :undoc-members:
```

## Reconstruction

```{eval-rst}
.. automodule:: pysinger.reconstruction.fitch
   :members:
   :undoc-members:
```