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In the wide world of software, squid is a proxy server used in high traffic websites, but this squid is Sean Eddy's utilites for general sequence reading.

This is only available on the biotime machine.


Its list of executable is as follows:

  • compalign
  • alistat
  • afetch
  • shuffle
  • sfetch
  • seqstat
  • seqsplit
  • revcomp
  • compstruct
  • weight
  • translate
  • sreformat
  • sindex

For the library, a static one is created and somehow the system recognises the -lsquid linking direction ... perhaps because /usr/local/lib is a very standard location, in an unusual location, it may not be so easy.