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.

All documentation is on fourierseq in: /usr/local/genome - consed in particular is only documented in a lengthy text document called "README_consed.txt". It has wonderful examples - please go through them before trying your own assembly project.

To run on an ace file from Mira or Newbler - there are two ways to get the assembly to open in consed:

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.

BUT you can't use many consed features unless you either run Newbler with the -consed option. We currently don't have a good option for converting Mira output cleanly to consed - SPHS hasn't researched this enough... any user solutions out there?

If you do use the -consed option with Newbler, follow the instructions in README_consed.txt to re-format it's output for use wiht consed (this isn't perfect...)