Muscle
Muscle is a fast program for high-quality multiple sequence alignment (MSA).
Responsible person: User:Joel Hedlund (NSC)
Compilation
Benchmarks at NSC have shown that Intel compilers seem to produce more efficient Muscle binaries than does gcc, and in particular when using interprocess optimisations (-ipo), which can more than double the execution speed.
However, as Muscle relies heavily on floating point arithmetics, and as such is sensitive to subtle changes in architecture and compiler versions, the alignments produced may not be identical to the ones produced by the official gcc-built binary distribution. The discrepancies have been noted and judged non-critical by NSC and Robert Edgar (author of the Muscle software), but if you rely on bit equivalence in the results, you should use the official precompiled binary distribution instead.
NSC is currently investigating the possibility of making available a freely distributable binary release compiled with icpc -O3 -ipo, which will be available at this location shortly, if all goes well.
