SMCSMC, short for Sequential Monte Carlo for the Sequentially Markovian Coalescent, is a method for estimating ancestral population size and migration history from sequence data. It has several advantages over comparable methods, especially when you are interested in analysing complex demographic models. The method uses a particle filter to sample from the posterior distribution of trees along the sequence and Variational Bayes to infer epoch specific demographic parameters over a given number of iterations. Please see the linked documentation for more detail, or check out the code on Github.
3 years, 8 months ago passed
.. image:: https://readthedocs.org/projects/smcsmc/badge/?version=latest :target: https://smcsmc.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status
<a href='https://smcsmc.readthedocs.io/en/latest/?badge=latest'> <img src='https://readthedocs.org/projects/smcsmc/badge/?version=latest' alt='Documentation Status' /> </a>
demographic-inference, particle-filter, population-genetics