C version, 150 times faster !

I used to use perl to implement to algorithm that alan and I are
working with. The performance is OK as for 5300 scaffolds it takes
70-80 minutes to complete the full comparison. I would not have thought
of re-write it in C if Leon did not ask me for a performance senimar in
the near future.

For
this seminar, I would like to have a real-case CPU-intensive program to
work with SHARK tool, and this gene duplication tool would be perfect
for it. It took me two days to re-write it in C (isnt's it amazing that
I have not touch C for almost 3 years).

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