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Now I'm working on the command, Mafft.

This command's usage is like below.

mafft in > out

as you can see, command line contains redirection operator.

This command line on windows os, it works.
This command line on linux shell prompt input directly, it works.

But if I run it through java Runtime().getRuntime().exec("command string", null), it gives me nothing but errors below.

Unknown option: /home/test/msa.txt
Unknown option: >

Is there any way to use redirection operator in command line?

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