katarinaelez/bioinformatics-algorithms

Implementations of bioinformatics algorithms in Python

bioinformatics-algorithms

• hmm - Implementation of Hidden Markov Models
  • hmm_guide.ipynb is a guide for implementing the HMM algorithms (forward, backward and Viterbi)
  • hmm.py contains the implementations described in the guide
  • test.py contains an example of usage
  • utils.py contains some useful functions

Getting started

Requirements

Implementations are based on numpy arrays.

pip install numpy

In order to play with the guides make sure to install Jupyter Notebook.

pip install notebook

Installation

git clone https://github.com/katarinaelez/bioinformatics-algorithms

License

MIT @ Katarina Elez