HMM

How to run

• Install node
• Clone this repository
• Viterbi: run npm run start:viterbi
• Posterior Decoding: run npm run start:posterior-decoding
• Viterbi Training: run sh src/gene-hmm-train/viterbi-training-example.sh
• Baum Welch: run sh src/gene-hmm-train/baum-welch-example.sh

This is a small project that:

• Computes the most likely annotations of a sequence given an HMM (Viterbi algorithm).
• Computes the posterior-decoding (using the Forward and Backward algorithms).
• Inferring parameters for an HMM (using Viterbi training or Baum-Welch).

That project handled as an homework assignment for the course: "Algorithms in Computational Biology".