Learn to use the ClustalW2 resource at the EBI Toolbox site for performing multiple sequence alignments, or MSA. MSA allow us to analyze the evolutionary relationship between species on a molecular sequence level. As well, multiple sequence alignments can help us to identify functionally important positions in a sequence family by simply looking at the conservation of positions or motifs within the sequence data.
Download the example data file by clicking here.

You will learn:

  • some background and theory for multiple sequence alignments
  • how to conduct sequence alignments using
  • to understand and adjust the results of ClustalW2 alignments


This tutorial is a part of the tutorial group Alignment and comparison resources. You might find the other tutorials in the group interesting:

BLAST: Basic Local Alignment and Search Tool

FASTA: FASTA sequence algorithm

Entrez Gene: NCBI's Entrez tool for gene-centric information

Primer3: Pick primers from a DNA sequence.

DCODE: DCODE.org Comparative Genomics Developments, a collection of powerful comparative genomics tools

VISTA: Tools for Comparative Genomics

RefSeq: Provides molecular sequence records to help locate gene and protein data.


EBI : This category includes all resources maintained at the European Bioinformatics Institute (EBI)

Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.


What's the Answer? (publication quality alignment images): This week's highlighted question is from the Bioinformatics subreddit. And I'm using it because it made me laugh. I dare someone to name their alignment tool "Fancy Pants". That said, it did provide li...

Video Tip of The Week: Jalview for multiple sequence alignment editing and visualization: The multiple sequence alignment editing question recently on our What's the Answer? feature was popular. We have covered MSA editors in the past, and we include a bit on Jalview in our Clustal tutorial...

Otto West: Apes don't read [genomics]: Otto West: Apes don't read philosophy. Wanda: Yes they do, Otto. They just don't understand it. --A Fish Called Wanda Some of you remember that last year we were treated to a strange case of DNA denial...

Tip of the Week: Tweaking those alignments: This week's tip introduces a nice feature and tool of the Viral Bioinformatics Resource Center (VBRC). There are a lot of great tools at the VBRC to search and analyze hundreds of viral genomes. Most, ...


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