Start clustalx by double-clicking the icon;
load globin.pep into the program;
calculate an alignment and save the result under different names in different formats
possible. Using a text editor (MS Word) and a non-proportional font, inspect the different
formats.
*.MSF is read by GCG; *.PIR output is like FASTA - format, but the seq. all have equal
lengths, you have to merge the first and second line in order to be FASTA compatible (you
also could use the GDE format and using a text editor replace % with >).
Phylip (*.phy) is the "new" phylip - interlaced format.
You can use the input/output options to reformat an alignment. Some programs require
specialized formats. You can use a text editor like MSWord to get your alignment into the
desired format, but things are certainly much easier, if you start out with a format close to
the desired one.
Hint: Often you do not want to use the complete alignment, but only those portions which
are sufficiently conserved. You can take a file in clustal format (*.aln) and delete columns
with a text editor (in MSWord pressing down the Alt key before clicking the mouse
switches to column mode -- to see the alignment, you often need to decrease the font size
and select a non-proportional font in your editor!). Although the different lines in the
resulting alignment have different lengths, clustal reads in the aligned sequences correctly,
and you can output the shortened sequences in any desired format you want.