I'm just curious if anybody can suggest command line programs that are designed to be truly parallelized?

I found a great post on running serial programs in parallel with GNU parallel: Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them

However, instead of using tricks to run serial programs in a parallel fashion, is there anything out there that can be run in parallel directly?

I'm mainly interested in programs used for chip-seq and rna-seq workflows. For example, I think STAR aligner can handle parallel processes, but I believe common tools like tophat, MACS, and cufflinks are all serial at some point.

Thanks in advance for any input.
Since you asked for tools for the analysis of RNA-seq and ChIP-seq data: there's [deepTools][1], [seqminer][2] and [spark][3] that all allow you to make use of multiple processors. I only have worked with deepTools though and of course, I think they're pretty great and useful (I helped develop them)

 [1]: http://deeptools.github.io/
 [2]: http://bips.u-strasbg.fr/seqminer/
 [3]: http://www.sparkinsight.org/