[Bioperl-l] Re: Trees as graphics

[Jason Stajich]

I would really suggest treeplot.

You specify the bootstraps as the label for internal nodes like this.
(((A:0.1,B:0.2)100:0.6),D:0.4),100:0.30);


Treeplot version 0.7
Developpment: Olivier Langella
CNRS UPR9034 Laboratoire PGE
e-mail: langella at pge.cnrs-gif.fr
Web: http://www.cnrs-gif.fr/pge/bioinfo

USAGE: treeplot SOURCE DESTINATION -[options]
DESTINATION is a postscript file (output.ps) by default.
to produce other format, choose one of these extensions:
.ps ==> Postscript
.ai ==> Adobe Illustrator
.svg ==> Scalable Vector Graphic
.cgm ==> Computer Graphic Metafile
.hpgl ==> Hewlet Packard Graphic Language
.fig ==> xfig file
.gif ==> gif image file
.pnm ==> PBM Portable aNy Map file

OPTIONS for treeplot
-t rect
drawing rectangular cladogram
-t phylogram
drawing phylogram
-nb
no bootstrap values
-og 'LIST'
-g 'COLOR' 'LIST'
where LIST is a list of OTU's (separated by spaces)
COLOR is a name of color (in english) or an rgb code (example: '255 0 0'
for red)


Other places to ask could be
bionet.molbio.evolution bionet.molbio.software I guess.

On Mon, 22 Sep 2003, basm101 wrote:

> Thanks for the advice all.
> Sorry if this follow-up isnt about bioperl - is there another discussion
> board you guys use for general questions
> about bioinformatics programs ?
>
> Does anyone know if it is possible using PHYLIP to output postscript
> files that include bootstrap values ?
> I have been trying using drawgram to output postscript files. However,
> when I preview the tree (which had been
> generated via seqboot->protdist->neighbor->consense) the bootstrap
> values that I can see in TreeView
> are no longer there.
>
> I will have a go at using ImageMagick and the Perl interface to it.
>
>
> Thanks,
> basm101
>
>
>
> Donald G. Jackson wrote:
>
> > basm101,
> >
> > to follow up on Jason's post -
> >
> > Phylip's drawgram program will output postscript.  If you just want to
> > change the format, the 'ps2gif' program (part of Ghostscript -
> > standard on most linux distros, available for Windows) is the easiest
> > way.  I use ImageMagick's 'convert' program (www.imagemagick.org??)
> > which lets me add legends and headers too.
> >
> > Don Jackson
> > BMS Bioinformatics
> >
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu