 Dear students, in this module I am going to talk about Clustall W. So, Clustall is essentially a tool for doing multiple sequence alignment and you can use progressive approaches towards MSA. So, let's take a look at the background. So, as I just mentioned that multiple sequence alignment involves alignment of sequences in such a way that you can extract the most similar sequences first and then repeat this process for other sequences such that all the sequences end up in an alignment. The progressive alignments are used. So, this entire process is essentially an iterative process and therefore we call it the progressive alignment. Towards doing this online you have the Clustall W which is an online tool which was developed by EMBL and EBI that is European Molecular Biology Laboratory and European Bioinformatics Institute. There are two modes in which this program can run. The first mode is the slow and accurate while the second is fast and approximate. So, if you want to use the slow mode towards an optimal alignment then you will get better results. While if you want to just have an idea of the alignment you can use the fast alignment but it will only give you approximate results. So, the Clustall W can help create multiple alignments. It can also optimize existing alignments for you. That is if there were some alignments which you wanted to modify in order to look at the relationship in a different way you can also do that. You can create profile analysis that is within each portion of the sequence you can see how the profile of the secondary structure of protein for example varies amongst multiple sequences and then you can use the MSA to create phylogenetic trees as well. So, the Clustall W is very easy to use. So, to start with you need to know how to input your data and to input your data you can either use faster format or you can put in the protein IDs as well or the IDs for the genes and once you input this information there are a set of parameters that you need to set before doing the multiple sequence alignment. So, let's take a look at the online version. Here at this URL you can access Clustall W so this is the front page for the software and you can put your sequences here and compare them or you can simply input the IDs here as well. More so you can upload an entire file of IDs or sequences of course in this format and you can execute multiple sequence alignment. If you want to tune your search or alignment you can look at the detailed parameters that are given here. So, to start using Clustall W you can simply use the default parameters that are already given here but later once you gain experience you can modify these set of parameters and optimize your search. So, for fast and approximate search you need to specify the window size so it will approximate it. To this window the gap penalty needs to be given as well as the K tuple word size. That is the comparison will be one amino acid at a time and so on. So, for the slow and accurate method you don't have to specify the window size or the word size you simply specify the gap open penalty and the gap extension penalty and you select the weight matrix or the scoring matrix. For proteins you can use blossom block substitution matrix and in this way you can set up your slow and accurate alignment. So, these parameters once input can help you execute the MSA. Besides Clustall W there are several other tools that are also available for you to use such as those listed here. So, I will quickly go over them. So, here is Clustall W or Clustall X now. The next version for the Clustall Omega is also available online. So, you can use that or if you are a novice you can also use tea coffee. So, this is a progressive alignment approach as well amongst many others. So, you can keep this list for your reference. So, in conclusion Clustall W can be used to perform multiple sequence alignment and you can set up multiple parameters to tune your alignment results. The latest version of Clustall is the Clustall Omega which is also available online and you can use it if you really want to have the best algorithm to align your sequences. So, before you get into using Clustall remember there are two approaches the fast and the slow. The slow one will give you accurate results and the fast one will only give you approximate results. So, if you are just comparing sequences on a large scale you may want to use the fast alignment but if you want to look at specific residues in a very exact way you may opt for the slow alignment process. Thank you.