This Microsoft Word macro
converts a ClustalW alignment file into a text file that you can open with PAUP*.
This
link contains
the Word macro. To install it just follow these easy steps:
1. Open it with Microsoft
Word, highlight everything and copy it.
2. Click on the tools bar and select macro and
then macros again.
3. Click on the create button if there is not
any macro installed already. Just give it a name, whatever. If there are macros
already installed, click on edit. In any case a window opens where you can paste
the new macro at the end of the text.
4. Close this window and you are ready to go.
5. To run the macro, open the alignment, pull
down tools, then select macro, macros again and choose the macro PAUP. Run it
once and it
will suggest where the alignment should start and end in a way that there are no
missing bases. Run it again to edit the alignment. Save it as text file and
change the extension to ".nex" before opening it with PAUP.