Installing MUSCLE

We use the sequence alignment tool MUSCLE in one section of the course. This can be installed as follows:

Linux/macOS installation

MUSCLE is available through Bioconda (which should already be set up on your machine):

conda install muscle

Windows installation

At the time of writing, MUSCLE is not available through Bioconda for Windows.

  1. Open http://drive5.com/muscle/downloads.htm with your web browser.
  2. Download the latest Windows Intel i86 binary, currently muscle3.8.31_i86win32.exe. This will be placed in your Downloads directory.
  3. In git bash change to your home directory with the command cd.
  4. Create a new directory called bin with the command mkdir bin.
  5. Copy the MUSCLE program to this new directory with the command cp Downloads/muscle3.8.31_i86win32.exe bin/muscle.exe. This creates a new command called muscle which runs the alignment program.
  6. Test that the program can be run by executing the command muscle in the terminal.

In total, the sequence of commands will be:

$ cd
$ mkdir bin
$ cp Downloads/muscle3.8.31_i86win32.exe bin/muscle.exe
$ muscle

Note

The $ sign should not be typed - this indicates the command prompt you will see on your screen.