An easy way to do protein sequence multiple alignments is by using ClustalW2 and presenting the alignment using JalView.
ClustalW2 is one of the most commonly used multiple alignment tools for alignment of both protein and DNA sequences.
1. Go to ClustalW2 website and enter your query sequences (in any of the supported formats like FASTA).
2. Choose .aln as the output format. You can obtain the output either by email or interactively.
Here is a sample .aln output:
This is a good software to view multiple alignments using colors and shading to highlight different characteristics of the sequences like hydrophobicity, percentage identity etc. It is a free software and can be downloaded here. By default Jalview opens some sample alignment files but don't worry about that.
1. Open the .aln alignment file from the main Jalview window. It also allows opening and adding files to the alignment in fasta, pdb and other formats.
2. You can do all sorts of formatting to the alignment file as required. For e.g., in the 'View' tab deselect 'Show Annotations', in the 'Format' tab select 'wrap' and in the 'Colour' tab select clustalx. This is how the output appears:
(Notice that here the pairwise alignment is colored on the basis of residue type (e.g. basic residues K and R are shown in red while nonpolar are marked blue). You can save the type of formating you prefer by changing the default settings. (Tools | Preferences)
3. To save the alignment as an image, go to 'File' and select 'Export Image' as PNG.
Jalview also allows doing the alignment using various web servies like ClustalW, MAFFT etc. (Web Service | Alignment |ClustalW )