How to align DNA sequences in Clustal

Alignment is a very important step before you start your phylogenetic analysis. It helps to understand the evolutionary relationship between sequences/taxa included in the study by observing events such as insertion and deletion. To be able to do that, you need to have homologous alignment. One way to do that is by using the available free online tools using Clustal Omega website.

1- Go to the official website of Clustal: https://www.ebi.ac.uk/Tools/msa/clustalo/

2- File out the first step required which is shown as the following:

Choose what kind you data are belong to Protin? DNA? RNA?.

Once you choose your data categories, you need to copy and pest all your sequences in the box. It is important to have the right format of your sequences before you pest them in the box. Here is an example of 2 sequences.

>HBA_HUMAN Hemoglobin subunit alpha OS
MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH
GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLL
SHCLLVTLAAHLPAEFTP AVHASLDKFLASVSTVLTSKYR


>HBA_MOUSE Hemoglobin subunit alpha OS
MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHG
SAQVKGHGKKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLS
HCLLVTLASHHPADFTP

Note that, the “>” symbol before the name of the sequence data (HBA_HUMAN Hemoglobin subunit alpha OS) and the sequence data are in another line.

Optional, you can upload your sequence file instead of posting them in the box and change the necessary parameters based on the file you uploaded.

3- Once you finish, you can submit your alignment process and you can choose to notify you by the email

You are done!! Good job.

A few notifications you should know about this free service to align your data:

  • There is currently a limit of 4000 sequences or a maximum file size of 4MB of data.
  • MSA tool algorithms are NOT intended to produce genome synteny maps.
  • This is NOT a pairwise alignment tool. To align two sequences please select a service from the pairwise alignment tools section.

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