Phred, Phrap, Consed, cross_match, daev

The "conventional" sequencing tools Phred, Phrap, and Consed along with their helper programs are installed on Fourierseq.

Phred is version 0.020425.c
Phrap is version 1.080812
Consed is version 20.

To run on an ace file from Mira or Newbler - there are two ways:

1. Run

   consed -nophd -ace <file.ace>

   or
   1. create a directory and name it with your project name (test_consed, for example)
   2. In that test_consed directory, create the following directories (Exact naming) :
      chromat_dir
      edit_dir
      phdball_dir
      phd_dir
      sff_file
   3. Go into the edit_dir directory and place the 454Contigs.ace file in there. Run consed from this location by just typing

      consed
      

   4. When the screen pops up, it'll show a listing of the ace files and the contigs, choose one and open.