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I want to execute phylocon on a mac OS X lion but after changing the path and making the file executable, I get the error 'cannot execute binary file'. But the steps that I took to running the command worked fine on ubuntu 12.04 which is why i am confused.

command: PhyloCon-v3.linux

http://stormo.wustl.edu/PhyloCon/

Can someone please tell me how to fix this?

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The command file PhyloCon-v3.linux should tell you what it is. –  ott-- Feb 21 '13 at 21:41
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I assume you've grabbed PhyloCon-v3b.linux from their web site. That's a Linux executable, it won't run on Mac OS X.

Instead, you need to grab the source code and compile it yourself. Extract the source code into an empty directory, then, if you're lucky, running make will compile it.

Note that it doesn't compile cleanly on my Linux box; it appears to use some questionable not-quite-C syntax which my modern GCC is not accepting. It appears easy enough to get to compile, by fixing a few declarations... Whether it works, I'm not at all qualified to answer.

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