POLYPHRED-3.5 INSTALLATION NOTES
1) Polyphred 3.5
Polyphred is an application which identifies putative heterozygotes
for substitution SNPs in fluorescence-based DNA sequence traces.
3) In order to run Polyphred you will need
Phred 0.961028 or later
Phd2fasta 0.971024 or later
Phrap 0.960731 or later
Consed 8.0 or later
For Phred, Phd2fasta contact
Brent Ewing (firstname.lastname@example.org)
For Phrap contact
Phil Green (email@example.com)
For Consed and PhredPhrap contact
David Gordon (firstname.lastname@example.org)
4) Make sure the required software is installed on your system.
5) Edit phredPhrap:
Uncomment the following line:
$polyPhredExe = "/usr/local/genome/bin/polyphred";
Change the 0 to 1
$bUsingPolyPhred = 1;
6) You can also run PolyTool, which is a graphical
interface for running PolyPhred see (POLYTOOL.doc).
7) In order to see polyPhred tags in Consed the contents of
POLYPHRED.CONSEDRC (included with this distribution in
given path) need to be added to the appropriate .consedrc file.
Consed resources can be specified in three different ways, in
a file named .consedrc in the top level of a user home directory
(user specific consed resources), in a file named .consedrc in
the edit_dir of project (project specific consed resources), and
in a file named by the environment variable CONSED_PARAMETERS
(system wide consed resources). For more information about consed
resources see the section named CONSED CUSTOMIZATION in the consed