[Bio-software] Phylip - WinXP

glykokalyx At hotmail.com via bio-soft%40net.bio.net (by glykokalyx At hotmail.com)
Fri Nov 17 11:09:18 EST 2006


Dear group-users!

I got a problem with phylip running on winXP. Maybe someone has an
idea. It would be appericated very much!

Here comes the problem...
After I have ran FITCH with my outfile from PROTDIS I get a tree-file
of the size of 0kb. Without much surprise I can't open the file with
the program Treeview. Of course, my original file contains sequences.

Version used:
OS: WinXP, Servicepack2, latest updates.
Phylip: 3.66.
ClustalX: 1.83
TreeView: 1.6.6

Following a step-to-step explanation how I proceeded:
1) Downloaded 3 protein-sequences from NCBI and saved them altogether
in one single text file in FASTA format (>name [new line] sequence).
2) Loaded the .txt-file into ClustalX and aligned them. Saved/exported
the alignment in a msf.-file.
3) Opened the .msf-file in Genedoc. Exported the sequences as a
.phy-file into the Phylip-directory (...\phylip3.66\exe).
4) Deleted all old outfile and infile in the Phylip-directory. Ran
PROTDIS (default settings used) with the .phy-file and got an outfile
(size of 1kb). Renamed the created 'outfile' to 'test'.
5) Ran FITCH (default settings used) with my 'test'-file. Got an
outfile-file (size of 1kb) and an outtree-file (size of 0kb!).
6) Trying to open the outtree file with TreeView the Error-message:
"Syntax Error: "477"" appears. Well, with 0kb no wonder.

After running PROTDIS my outfile-file looks like:
    3
putida      0.000000  0.713185  3.438244
LB400       0.713185  0.000000  3.052331
HD100       3.438244  3.052331  0.000000

And after FITCH it looks like:

   3 Populations

Fitch-Margoliash method version 3.66

                  __ __             2
                  \  \   (Obs - Exp)
Sum of squares =  /_ /_  ------------
                                2
                   i  j      Obs

Negative branch lengths not allowed

Maybe this spreads some more light on it.

I tried to install it on different winXP PC's. Installation was
performed with the administrator account. As well as the testing
itself. So, it should be not an issue of some missing rights.
We had all the programms running fine on windowsNT and windows2000.

If anyone could give a helping hand, that would be great!

If any information is missing I'd be happy to provide it.

Cheers for the help!

With kindest regards,
Janosch



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