You may find this easier using the graphical version of ClustalW 2: ClustalX2 (see http://clustal.org/clustal2/), rather than the command-line ClustalW 2, FWIW the download for MS Windows is: clustalx-2.1-win.msi. After installation you will have a program menu item for ClustalX2, which you can run. You then load the sequences to be aligned ("File" -> "Load Sequences"), and perform the alignment ("Alignment" -> "Do Complete Alignment"). By default the guide tree (.dnd) and alignment (.aln) files will be generated in the same directory as the file of input sequences, but you can change this when prompted if you want them to go somewhere else.
If you have to use the command-line version of ClustalW 2, then you will need to know the path to your input sequences and since the ClustalW 2 executables are not automatically added to the PATH, where ClustalW 2 was installed. A typical command line session would look something like:
> cd "C:\Users\username\Documents\My Documents\Data"
> "c:\Program Files (x86)\ClustalW2\clustalw2.exe" /INFILE=arf_seq.faa /ALIGN
Assuming that the
C:\Users\username\Documents\My Documents\Data directory contains the input sequence data to be aligned, in this case the contents of the
arf_seq.faa file of fasta formatted sequences. By default the output files are generated in the directory containing the input data, and are named after the input file (in this case
The same principle applies if you are using the interactive mode of ClustalW 2, except that you will need to know the complete path to the input sequence data file (e.g.
C:\Users\username\Documents\My Documents\Data\arf_seq.faa) in order to load the sequences. Again by default the output files will be generated in the directory containing the input file and will be named after the file. However this can be changed by using the prompts during the alignment process. Note that relative paths should be avoided if using the program menu item to start ClustalW 2 in interactive mode since these will be relative to the "Start in" directory specified in the shortcut used (typically the installation directory).
Please note that ClustalW 2 has largely be superseded by Clustal Omega, for most purposes the use of Clustal Omega is recommended.
For further assistance with the use of the Clustal series of multiple sequence alignment programs I suggest you contact the authors, see http://clustal.org/ for details.