latent_space_paper

Multiple sequence alignment using HMMER

HMMER installation:

1. Download HMMER from the official HMMER website.
2. Follow the installation instructions provided on the website or in the downloaded package.
3. To verify that HMMER has been installed successfully, run the following command in your terminal or command line:

   hmmalign --version
   

Run hmmalign:

1. Create an HMM profile from your seed alignment.

   hmmbuild ./data/PF01494_seed.hmm ./data/PF01494_seed.sto

2. Run alignment and output the result to a fasta file

   hmmalign ./data/PF01494_seed.hmm ./data/PF01494_input.fasta > ./data/PF01494_MSA.fasta