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Problems with Phylip tree plotting

Michael A Lonetto Michael_A_Lonetto at sbphrd.com
Fri Apr 18 09:56:32 EST 1997


Hello,

Not really a GCG question :-), but this is pretty easy to fix:

1) Phylip is limited to 10 character names, and truncates anything longer (if I 
recall correctly, it also drops hyphens and underscores).  This is often 
painful, but there's not much you can do but make sure your first 10 characters 
specify a unique name.  Then you can change  it in the output as below:

2) drawgram will output text in editable form if you specify a PostScript 
typeface instead of one of the built in fonts.  Postscript is case sensitive so 
you need to get the name exactly right (drawgram doesn't care what you put, it 
just saves it as a "setfont" command in the postscript output), eg:

Helvetica
Helvetica-Bold
Helvetica-BoldObllique

Check your printer documentation or use a printer utility to get a list of 
fonts.

The output will now have editable text.  You can thus fix it by search and 
replace in the text file, or, better yet, you can import it to Adobe 
Illustrator and edit it interactively (put in the long names and adjust 
position interactively) before printing.

Good Luck,

Mike Lonetto
SmithKline Beecham Pharmaceuticals R&D inc.
To: info-gcg @ net.bio.net @ INET
cc: (bcc: Michael A Lonetto)
From: cgovaert @ ulb.ac.be (Cedric Govaerts) @ INET 
Date: 18-Apr-97 01:30:44 PM
Subject: Problems with Phylip tree plotting
Categories: 

Hi

I'm aligning sequences with ClustlW and want to get the guiding tree plotted.
For this purpose, I create a "Phylip" tree with ClustalW and then
put it in drawgram, a Phylip program accessible in GCG8.
This works fine as long as I don't change the names in my tree file.
It appears that if I replace the accession numbers used to denominate the
sequences by more explicit names (so more large names) drawgram gives
only a part of the plotfile (the first braches and names). 

In the PostScript output, drawgram "draws" the letters as if they
were drawing objects, so I can't do any search and replace in the
PostScript file itself, it has to be done before.

Does anyone know about restriction in the size of the name in Phylip.

Thanks,

Cedric Govaerts

.................................................................
.       Cedric Govaerts                                         .
.       Institut de Recherche Interdisciplinaire                .
.       en Biologie Humaine et Nucleaire                        .
.       808, route de Lennik 1070 Bruxelles                     .
.       email : cgovaert at ulb.ac.be or cgovaert at dbm.ulb.ac.be    .
.       Phone : Int + 32 2 555 41 87 / Fax : 555 46 55          .
................................................................. 






To: info-gcg @ net.bio.net @ INET
cc: (bcc: Michael A Lonetto)
From: cgovaert @ ulb.ac.be (Cedric Govaerts) @ INET 
Date: 18-Apr-97 01:30:44 PM
Subject: Problems with Phylip tree plotting
Categories: 

Hi

I'm aligning sequences with ClustlW and want to get the guiding tree plotted.
For this purpose, I create a "Phylip" tree with ClustalW and then
put it in drawgram, a Phylip program accessible in GCG8.
This works fine as long as I don't change the names in my tree file.
It appears that if I replace the accession numbers used to denominate the
sequences by more explicit names (so more large names) drawgram gives
only a part of the plotfile (the first braches and names). 

In the PostScript output, drawgram "draws" the letters as if they
were drawing objects, so I can't do any search and replace in the
PostScript file itself, it has to be done before.

Does anyone know about restriction in the size of the name in Phylip.

Thanks,

Cedric Govaerts

.................................................................
.       Cedric Govaerts                                         .
.       Institut de Recherche Interdisciplinaire                .
.       en Biologie Humaine et Nucleaire                        .
.       808, route de Lennik 1070 Bruxelles                     .
.       email : cgovaert at ulb.ac.be or cgovaert at dbm.ulb.ac.be    .
.       Phone : Int + 32 2 555 41 87 / Fax : 555 46 55          .
................................................................. 









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