- 2001: Neurospora
- 2002: Mouse (first mammalian genome)
- 2004: Chimpanzee (first assisted low-coverage assembly)
- 2005: Dog (led to a paper in Nature)
- 2007: Horse
Over the years and with every new genome assembled (the number approaching/exceeding 100 genomes), the Arachne code base grew into a monster. When translating the source code into genomic DNA, a number of evolutionary features become apparent: at a genome size of 46 Mbp, we find that 57% of the sequence resides in repetitive 48-mers, indicating a recent explosion of repetitive elements. We are still in the process of classifying repeat families, but it is apparent that most of them have a functional role.
The first suggested name for this program was Ariadne, a woman from Greek mythology who is best known for providing the string to mark a path in the Minotaur's labyrinth. However, it turned out that this name was already taken by Ariadne Genomics. So the similar name Arachne was chosen instead. Arachne is another character from Greek myth: an expert weaver, skilled at turning disparate threads into a single tapestry in much the same way that WGA is supposed to work.