Muliple Sequence Alignment

For Multiple sequence Alignment you need Fasta sequence for this go to ncbi for nucleotide or at expasy server for protein sequence but now I am going to work with proteins so go to www.expasy.org
enter your query for which you want to retrieve the sequences
or you can also go to uniprot which in my opinion is easy to use and get fasta sequence so go to uniprot and enter protein hemoglobin and get different entries of this protein click them and get fasta sequence like this

and select many proteins and get their fasta formats like this
 click on fasta and http://www.uniprot.org/uniprot/P68871.fasta
copy and paste these fasta sequences of many proteins in a text file and collect all these sequences in a text document.
In this format I pasted my all sequences in my notepad

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ClustalW:

ClustalW is a general purpose multiple sequence alignment program for DNA and proteins it produces biologically meaning full multiple sequence alignments of divergent sequences it calculates the best match for selected sequences that lines up so that the identities and similarities and differences and evolutionary relationships can be seen via viewing cladograms or phylograms.

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Bioinformatics Tutorials Using ClustalW to do a multiple sequence alignment

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The Tools used in Bioinformatics

NCBI Map Viewer
For finding genes and gene products (RNAs and proteins) that interest you
BLAST
For finding genes or proteins with sequences similar to yours
ClustalW
For comparing your sequence with others, and lots of sequences with each other
Phylip
For making phylogenetic trees, which show how sequences are related to each other.
Treeprint
For printing phylogenetic trees
PSIPRED
For predicting the location of helices, pleated sheets, and transmembrane elements of proteins of unknown structure
Swiss-Model
For automated building theoretical structural models of your sequence based on known structures (homology modeling)
Deep View (also knows as Swiss-PdbViewer)
For seeing and exploring macromolecular models in three dimensions, and for manual and semiautomated homology modeling
PubMed
For searching ALL the literature of the life sciences
ExPASy (Expert Protein Analysis System
Not so much a tool as a tool box -- a very complete set of protein analysis tools

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