JalView (written in Java) is an alignment editor and can retrieve and display protein structure files as well. It is available from the Barton Group at the University of Dundee in Scotland
Jalview can align multiple sequences, but becomes quite slow when working with more than four or five sequences. For those cases, JalView can do multiple alignments by accessing the ClustalW web site directly.
When downloading Jalview, Use the "Install with InstallAnywhere" button on the download page. Choose the version for your operating system; if you're not sure whether you have a Java Virtual Machine already installed, select that version for your OS. Then select Run from the window that appears. Ask the installer to put an icon on your desktop. Start the program by clicking the icon.
To do an alignment in Jalview, choose File/Input Alignment/from File. Navigate to your sequence file and click OK. The result will look like this:
In the new window that has appeared, choose File/Add Sequences/from File. Navigate to your next sequence and click OK. (Any number of sequences can be added in this way.)
Select both sequences by holding down Ctrl and clicking on their titles. Then choose Calculate/Pairwise Alignments. The result looks like this:
Click the "View in Alignment Editor" button at the bottom of this window. You can now choose to color your alignment by any of a variety of schemes. I chose the Clustalx scheme, which assigns each amino acid a color. I then chose Wrap from the Format menu to produce:
You can save your alignment as a picture by choosing "Export Image" from the file menu; this gives you the choise of a web page (html), a Postscript file (eps) or a Word-compatible picture (png).
Multiple sequence alignments are done by reading in all of the files of interest and choosing Web Service; select your preferred server from the menu.
Here are links for a two page reference card for Jalview and a full tutorial by the authors of the program. I have printed out the reference card and put the pages back-to-back in a page protector for easy reference.
Here are the URLs for a number of web servers that will carry out alignments on sequences that you submit:
|STRAP (also does structure alignments)|
Easiest is to have your multiple sequences combined into a single file: simply use NotePad or any text editor. Paste one FASTA file after another into a single FASTA file (include the title lines), and use the upload feature. Alternatively, you can just copy and paste, one after the other, into the alignment window.
Allignments produced by any of these servers can be read into BioEdit or JalView and formatted to suit.