There are commonly used alignment programs such as muscle, blast, clustalx, and so on, that can be easily installed from the repository. In this article, we are going to install such software on Ubuntu 18.04 & 20.04.

Preparing system

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing alignment programs

• MUSCLE
  $ sudo apt-get install -y muscle
• MAFFT
  $ sudo apt-get install -y mafft
• Clustal Omega
  $ sudo apt-get install -y clustalo
• ClustalW
  $ sudo apt-get install -y clustalw
• ClustalX
  $ sudo apt-get install -y clustalx
• Dialign
  $ sudo apt-get install -y dialign
• MUMmer
  $ sudo apt-get install -y mummer
• NCBI-BLAST+
  $ sudo apt-get install -y ncbi-blast+
• EMBOSS
  $ sudo apt-get install -y emboss
$ sudo apt-get install -y emboss-lib
• HMMER
  $ sudo apt-get install -y hmmer
• JAligner
  $ sudo apt-get install -y jaligner

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These are a few commonly used alignment programs that can be easily installed from the repository in Ubuntu.