The octal-core AMD system reported gains in Red Hat Enterprise Linux 6.0 over Red Hat Enterprise Linux 5.5 and the rest, but on the Intel Core i5 system the performance was virtually unchanged across the five tested Linux operating systems.
The Intel Core i5 system was faster with Red Hat Enterprise Linux while the AMD system had not seen much in the way of changes.
The HMMer performance improved greatly between Red Hat Enterprise Linux 5.5 with GCC 4.1 and the Linux 2.6.18 kernel and now Red Hat Enterprise Linux 6.0 with GCC 4.4 and Linux 2.6.32. Between Red Hat Enterprise Linux 6.0 and the other recent Linux distributions, however, there was not any definitive leader.
Lastly, with MAFFT there are also reported improvements on both Intel and AMD systems when switching from RHEL 5.5 to RHEL 6.0.
With Red Hat Enterprise Linux 5.x using the Linux 2.6.18 kernel, EXT3, and GCC 4.1 by default, there's quite a number of areas in Red Hat Enterprise Linux 6.0 where the performance has improved measurably, assuming you had not manually built newer key packages for RHEL5. Using GCC 4.4, EXT4, and the Linux 2.6.32 kernel results in noticeable improvements in many areas except for a few where the disk performance falls due to the EXT4 file-system, but that should be because of additional safeguards to protect the drive's data.
For those interested in validating the performance of Red Hat Enterprise Linux 6.0 there is the Phoronix Test Suite with more than 130 automated benchmarks available to cater towards your particular workload and we are happy to help with your other individualized testing needs.