For eg: Here is Which programs are best with those benchmarks removed: http://benchmarksgame.alioth.debian.org/u32/which-programs-a...
This shows Perl higher up the chart with it being 49% better (on average) than Ruby.
Some other things to note:
1. Perl has never been fast with binary trees. But Ruby 1.8 is even worse (I recall it being many times slower than Perl at this). So hats off to the Ruby 1.9 VM guys because they've turned things around and now it's even out pacing Lua on this benchmark! - http://benchmarksgame.alioth.debian.org/u32/performance.php?...
2. Fasta in Ruby maybe twice quicker than Perl however it uses over 100 times more memory! This is be because it's inlining some code (eval) giving it a huge speed bump at expense of a bigger program footprint. If I do a port of this to Perl then this fasta.pl runs 2.6 times faster than alioth's perl version (which now means the Ruby version is about 30% slower than it's direct equivalent Perl version).
3. My make_repeat_fasta idiomatic subroutine is actually a little slower than the one in fasta.pl on alioth. So both my fasta.pl & alioth's fasta.rb programs could be speeded up more :)
4. I may even be able to shave a little bit more off fasta.pl time. Same might be true for spectral norm & binary-tree however the Perl versions aren't showing up on alioth site at moment :( ... IIRC, when I last looked at the perl binary-trees code on alioth a couple of years ago I was able to shave 10% off.
ref: My perl port of fasta.rb on alioth - https://gist.github.com/4675254