Quick Start Guide

Please follow these steps to quickly set up HMMvar.

  1. Download HMMvar package and pre-computed HMMs at the Downloads page.
  2. If you are using Linux or MAC OS, please go to the directory of the HMMvar package and install it by running the following commands.
  3. Prepare your input files (sequence file and variants file). You can find the formats of the input files here.
  4. Find the corresponding hidden Markov model from the HMM library you downloaded at step 1.
  5. Implement HMMvar by the command hmmvar -q <query filename> -v <variants filename> -hmmbuildout <HMM>
  6. Check the output file (<variants filename>.out). To interpret the output file, please refer to the instruction here.