Go Back   Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum > Molecular Research Topics Forum > Protocols and Methods Forum
Register Search Today's Posts Mark Forums Read

Protocols and Methods Forum Post Any Protocol, Method, Technique, Procedure or Tips / Troubleshooting for any Molecular Biology Technique.


Phylip - WinXP

Phylip - WinXP - Protocols and Methods Forum

Phylip - WinXP - Post Any Protocol, Method, Technique, Procedure or Tips / Troubleshooting for any Molecular Biology Technique.


Reply
 
LinkBack Thread Tools Display Modes
  #1  
Old 11-17-2006, 03:41 PM
glykokalyx@hotmail.com
Guest
 
Posts: n/a
Default Phylip - WinXP



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.

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

Reply With Quote
  #2  
Old 11-17-2006, 03:53 PM
glykokalyx@hotmail.com
Guest
 
Posts: n/a
Default Phylip - WinXP

Sorry for just posting again.
I forgot to give the information of my outfile-files.

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.

Thanks again for your help!

Regards,
Janosch

Reply With Quote
  #3  
Old 11-17-2006, 03:55 PM
Don Gilbert
Guest
 
Posts: n/a
Default Phylip - WinXP

You may get more answers via the sister Bionet newsgroup
bionet.software (email [Only registered users see links. ] )
with this and other bio-software questions, including from Joe Felsenstein,
Phylip's author -- Don Gilbert

In article <1163778077.107193.278040@e3g2000cwe.googlegroups. com> you write:

--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- [Only registered users see links. ]/
Reply With Quote
  #4  
Old 11-17-2006, 04:07 PM
glykokalyx@hotmail.com
Guest
 
Posts: n/a
Default Phylip - WinXP

Thank you for the notice, Don! I'm going to cross-post it at the other
group then, too.
Regards,
Janosch



Reply With Quote
  #5  
Old 11-17-2006, 08:45 PM
glykokalyx@hotmail.com
Guest
 
Posts: n/a
Default Phylip - WinXP

Hello Jayakumar,

thank you for your reply!
Actually, I've just tried it with Treeview all the time. As I know it
from the time when we had Phylip running on winNT/2000.
I will try it with Drawtree now, though. Thanks to your hint!
Just baffled that Treeview cant open it, though it's supporting phylip
files.

Thank you again for your helpfull post!

Regards,
Janosch



Reply With Quote
Reply

Tags
phylip , winxp


Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On

Forum Jump

Similar Threads
Thread Thread Starter Forum Replies Last Post
Bootstrapping microsatellites with Phylip ronf Bioinformatics 0 11-13-2008 08:38 AM
PHYLIP and DNADIST Joe Felsenstein Microbiology Forum 0 06-30-2007 02:01 AM
Phylip - WinXP Jayakumar, R Protocols and Methods Forum 0 11-17-2006 08:34 PM


All times are GMT. The time now is 06:28 AM.


Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.
Copyright 2005 - 2012 Molecular Station | All Rights Reserved
Page generated in 0.13562 seconds with 16 queries