[Bioperl-l] protdist changes

Jason Stajich jason.stajich at duke.edu
Thu Sep 29 22:02:11 EDT 2005

George are you running phylip 3.61 ?

The order of distance methods for me is:

Protein distance algorithm, version 3.61

Settings for this run:
   P  Use JTT, PMB, PAM, Kimura, categories model?  Jones-Taylor- 
Thornton matrix
   G  Gamma distribution of rates among positions?  No
   C           One category of substitution rates?  Yes
   W                    Use weights for positions?  No
   M                   Analyze multiple data sets?  No
   I                  Input sequences interleaved?  Yes
   0                 Terminal type (IBM PC, ANSI)?  ANSI
   1            Print out the data at start of run  No
   2          Print indications of progress of run  Yes

Which means in the PhylipConf.pm file would need to be this:
       'MODEL'  => {
           'PMB'        =>"P\n",
           'PAM'        =>"P\nP\n",
           'KIMURA'     =>"P\nP\nP\n",
           'CAT'        =>"P\nP\nP\nP\n",
           'JTT'        =>"Y\n",

I've checked this in, let me know if it works?

Jason Stajich
Duke University

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