HMMER tool is used for searching sequence homologs using profile hidden Markov Models (HMMs) [1]. It is also one of the most widely used alignment tools. In this article, we will install the latest HMMER package on Ubuntu.

Preparing system

Let’s update and upgrade the system first.

Open the terminal (Ctrl+T) and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading HMMER

We are downloading the latest stable version of HMMER (v3.3.1). You can select other versions here. Move inside the directory where you want to download the software. Open a terminal and copy-paste the following commands.

$ cd Downloads/

$ wget http://eddylab.org/software/hmmer/hmmer-3.3.1.tar.gz

Installing HMMER

Untar the file and install.

$ tar xvzf hmmer-3.3.1.tar.gz

You will see a new directory in your ‘Downloads‘ namely, ‘hmmer-3.3.1‘. Move inside this new directory.

$ cd hmmer-3.3.1/

Now, install using the following commands.

$ ./configure

$ make

$ make check

$ sudo make install

After its completion, move inside another directory, namely, ‘easel’, and install that as well.

$ cd easel/

$ sudo make install

It will take a few minutes to finish depending on your system’s configuration. After that, the HMMER package is completely installed on your system.