Kiyoshi Gotow gotow at VIR.BEKKOAME.OR.JP
Fri Feb 23 03:28:35 EST 1996

At 15:43 96.2.22 -0700, David Frederiksen wrote:
>I am having some trouble using this software package on my 
>Macintosh.  I recently downloaded the PPC executables and tried to 
>input a 11 species protein sequence, aligned using clustal W and 
>saved in a philyp format, but the input file could not be read.  I 
>continued to get missing operand errors.  Can some one please help 
>me determine the input command for protml ...
>  These are the commands I have tried in the argument window 
>("surfaceprotein" is the input file name):
>protml -I surfaceprotein
>protml [-I] surfaceprotein
>protml surfaceprotein
>   Any information would be greatly appreciated.

When you see the argument window, the program "protml" is already running. 
The first word "protml" is unnecessary.  In addition to the input file
format command "-I", you need to specify the model of analysis and other
parameters that you want to use in the maximum likelihood method.  The file
"PROTML.EXA" in the package may give you some idea of the model, search
strategy or mode, and others given by ProtML 2.2.

I hope this helps.

Kiyoshi Gotow, Ph.D.
Department of Human Life and Culture
Junior College, Seitoku University
gotow at vir.bekkoame.or.jp

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net