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 CSE 490MT: Local Copies of Software
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Where to find FootPrinter and ClustalW

FootPrinter and ClustalW have been installed on the Instructional Lab Linux systems and the Instructional Project machines (amlia, kiska, and umnak). FootPrinter is located in the /usr/local/FootPrinter directory. ClustalW is located in the /usr/local/bin/clustalw directory.

Recommended mode for producing a phylogeny from ClustalW

Run the following command line arguments: 
clustalw -infile=filename.txt
clustalw -tree -infile=filename.aln
The tree will be created in filename.ph

Note on Instructional Project machines as servers

Note that the Instructional Lab Linux machines should not be treated like servers. If you are not physically sitting at one of these machines, do not log in to one of them and run a process. If you need to work from a Windows machine or from home, log in to one of the Instructional Project (as opposed to Instructional Lab Linux) machines listed above to do your work.

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