Indeed. And since IPC::System::Simple gives access to the list form for exec, might as well use it to save us from creating shell literals from the args.

use IPC::System::Simple qw( capture );
my $result = capture(
   blastall => (
      -p => 'blastx',
      -d => $baz,
      -i => $foo,
      -o => $bar,
   )
);
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But looking at what those args are, it seems to me that it makes no sense to use backticks, capture or capturex with -o. system (or IPC::System::Simple's version) would be more appropriate.