# Multiple Sequence Alignment Analysis¶

Warning

You require the optional dependency SciPy package to use this script. If you are unsure if it is installed on your system, refer to the Installation documentation

If you would like to analyse a Multiple Sequence Alignment (MSA) file, you can do so using ConKit’s provided script, which is called conkit-msatool.

\$> conkit-msatool toxd/toxd.a3m a3m


The call above analyses the toxd.a3m MSA file, which is in a3m format. This call with will procude the following output:

Input MSA File:                   toxd/toxd.a3m
Input MSA Format:                 a3m
Sequence Identity Threshold:      0.7
Length of the Target Sequence:    59
Total Number of Sequences:        13448
Number of Effective Sequences:    3318
Sequence Coverage Plot:           toxd/toxd.png


The output tells you the file and format you have provided. It also prints which identity threshold was used to compare sequences during the analysis. Furthermore, it tells you the total number of sequences in your alignment and the number of effective sequences, or depth, of your alignment. Finally, this script will produce a plot that illustrates the coverage of your alignment in individual positions. The plot is shown below: