print large trees and tree output
Saskia Bode
Andrew Rambaut
I think you are underestimating the practicality of PDF. PDF is a
widely supported and editable vector format. There are plenty of
(free) programs that can convert to other vector formats (including
SVG). Many vector editing programs (including Adobe programs and
CorelDraw) can open PDF directly for editing (Adobe Illustrator can
use it as a native format). The main problem is that Microsoft (for
obvious political reasons) hates PDF and tries its best to make them
look bad. If you want to import into PowerPoint then using a PDF to
WMF converter will usually do the trick.
That said, I am looking at putting other export formats into FigTree
but it relies on 3rd party libraries because life is too short to
write my own graphic export functions.
Andrew
On 29 Jan 2008, at 10:57, F P D Cotterill wrote:
> The lack of practicable export facilities in Figtree is probably the
> most serious deficiency weakening Beast....otherwise a truly
> excellent software suite. Figtree desperately needs an svg format
> facility (like SplitsTree) so one can edit a vector graphics file in
> Adobe or Coreldraw (Powerpoint is too mickey-mouse...).
>
> A feasible way - albeit still a painful route - is export the tree
> from Figtree as a pdf; then save that pdf (working in full version
> of Adobe Acrobat) as a jpg; then import said graphic into Coreldraw
> using the CorelTrace Tool....With the aid of some rich language
> [:-) ] this procedure can "vectorize" the lines, which you can then
> edit to different thicknesses & colours etc. Unfortunately, the text
> becomes traced too, so taxon names cannot be edited as fonts in the
> graphics package (so retype all taxon names....yawn).
>
> A possible alternative - this may be feasible via nexus or Newick
> format - is to get the SplitsTree v4.8, to draw the tree, which can
> then be exported as an image in svg format (one of this package's
> many wonderful features). This imports straight into Coreldraw...one
> only has to ungroup the graphic, then Select all text/; cut & paste
> into one or more separate layer (where it's easier to edit etc).
> With such complicated graphic files, it also helps to cut & paste
> clades into their own layers where they can changed swiftly into
> different colours etc.
>
> Coreldraw X3 uses the PowerTrace facility under the Bitmap command
> suite.
>
> hope this makes sense
>
> cheers
>
> Woody
___________________________________________________________________
Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624
F P D Cotterill
Thanks for rapid feedback and correcting me on this....Life sure will be easier, now, with managing graphics...and all my colleagues have suffered same hassles in ignorance of how to edit pdfs :-) !!! Concur on the negative fallout of M'soft "policy"
Thanks for all your hardwork and support of this great package
all best
Woody
--
F.P.D. Cotterill, Phd
AEON - African Earth Observatory Network,
and Department of Geological Sciences,
and Department of Molecular and Cell Biology,
University of Cape Town, Rondebosch 7701,
South Africa
fenton.c...@uct.ac.za
++27-21-650 3165 (w)
083 432 3556 (cell)
"Nilli illigitimi carborundum" from the dog-Latin >> "Don't let the bastards grind you down"
F P D Cotterill
The lack of practicable export facilities in Figtree is probably the most serious deficiency weakening Beast....otherwise a truly excellent software suite. Figtree desperately needs an svg format facility (like SplitsTree) so one can edit a vector graphics file in Adobe or Coreldraw (Powerpoint is too mickey-mouse...).
A feasible way - albeit still a painful route - is export the tree from Figtree as a pdf; then save that pdf (working in full version of Adobe Acrobat) as a jpg; then import said graphic into Coreldraw using the CorelTrace Tool....With the aid of some rich language [:-) ] this procedure can "vectorize" the lines, which you can then edit to different thicknesses & colours etc. Unfortunately, the text becomes traced too, so taxon names cannot be edited as fonts in the graphics package (so retype all taxon names....yawn).
A possible alternative - this may be feasible via nexus or Newick format - is to get the SplitsTree v4.8, to draw the tree, which can then be exported as an image in svg format (one of this package's many wonderful features). This imports straight into Coreldraw...one only has to ungroup the graphic, then Select all text/; cut & paste into one or more separate layer (where it's easier to edit etc). With such complicated graphic files, it also helps to cut & paste clades into their own layers where they can changed swiftly into different colours etc.
Coreldraw X3 uses the PowerTrace facility under the Bitmap command suite.
hope this makes sense
cheers
Woody
Will Fischer
(on Mac OSX v 10.4, acrobat version 8.1.1). You can then alter the
"Tile Scale" to whatever percent you like. (At 1600%, my 1 page pdf
would be spread out over 56 pages! Yeeee-ha!)
There are probably some ghostscript options as well.
______________________
Will Fischer, Ph.D.
net: wfis...@lanl.gov
tel: 505-665-4149
fax: 505-665-3493
Group T-10, MS K710
Los Alamos National Laboratory
Los Alamos, NM 87545
USA
Julian W Tang
I'm really glad someone asked this question.
The manipulation and presentation of phylogenetic trees is not well covered in workshops.
I agree with Andrew in that the PDF format is very versatile, but that it does not really respond to 'reduction' very well! I have used PDF formats (with the full version of Adobe Acrobat - which is essential) of trees drawn using different software from Treeview to NJPlot and now Figtree to label the branches with bootstrap values and to highlight any interesting branches.
At the moment I have some beautiful influenza trees in PDF format drawn in Figtree, where I have used the Acrobat editing functions to label the branches with significant bootstrap values and to highlight the interesting branches. However, the PDF files show continuous trees containing 300 to 600 sequences (you can just keep scrolling down the page), which are beautifully labelled/highlighted, but which cannot fit into a side of A4 for publication and be legible.
What I am thinking of now is to submit these complete trees as 'On-line Material' for those who are interested, and to use Acrobat's snapshot function to copy and paste small windows of the tree containing branches that can be referred to in the main text for Results and Discussion.
Alternatively, the whole tree can be represented as a sort of 'cartoon' with lines and blobs to show the overall topology, that does not have any sequence names on the branches. Even if there are names, they will be too small to read, but they just become blobs in the overall tree toplogy.
See some examples of these approaches in these freely accessible papers attached here:
Date: Sat, 26 Jan 2008 19:23:47 +0000
From: snsa...@gmail.com
To: beast...@googlegroups.com
Subject: print large trees and tree output
Matthías Macé
If large tree representation is a relevant issue, another choice could to edit the vector format (e.g. by exporting the pdf to eps) and use the flash format in order to make a 'cartoon' with collapsed branches that can be deployed by clicking onto them. This can be achieved by the scripting possibilities within the flash format. Another interest is that flash reader comes with most of the web browsers.
Moreover, even if this is not related with the topic, Flash can be used to create slideshows that are far more flexible than with powerpoint or openoffice (and without font bad surprises when you are working on a mac or linux and have to present on a windows platform...)...
Best,
MM
En/na Julian W Tang ha escrit:
Dear Saskia
I'm really glad someone asked this question.
The manipulation and presentation of phylogenetic trees is not well covered in workshops.
I agree with Andrew in that the PDF format is very versatile, but that it does not really respond to 'reduction' very well! I have used PDF formats (with the full version of Adobe Acrobat - which is essential) of trees drawn using different software from Treeview to NJPlot and now Figtree to label the branches with bootstrap values and to highlight any interesting branches.
At the moment I have some beautiful influenza trees in PDF format drawn in Figtree, where I have used the Acrobat editing functions to label the branches with significant bootstrap values and to highlight the interesting branches. However, the PDF files show continuous trees containing 300 to 600 sequences (you can just keep scrolling down the page), which are beautifully labelled/highlighted, but which cannot fit into a side of A4 for publication and be legible.
What I am thinking of now is to submit these complete trees as 'On-line Material' for those who are interested, and to use Acrobat's snapshot function to copy and paste small windows of the tree containing branches that can be referred to in the main text for Results and Discussion.
Alternatively, the whole tree can be represented as a sort of 'cartoon' with lines and blobs to show the overall topology, that does not have any sequence names on the branches. Even if there are names, they will be too small to read, but they just become blobs in the overall tree toplogy.
See some examples of these approaches in these freely accessible papers attached here:
Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC. Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog. 2007 Sep 14;3(9):1220-8.Hué S, Pillay D, Clewley JP, Pybus OG. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4425-9.Hope this helps,Julian
Dr Matthias Macé, Vet. Med. Post-Doctoral Fellow / Chargé de Recherches Cliniques CHU !! Attention, nouvelle adresse !! !! Take care of the new address !! INSERM U563, Centre de Physiopathologie de Toulouse Purpan Département Génétique Génétique des troubles de la réfraction et des épithéliums oculaires-Eq. F Malecaze/P Calvas C.H.U. Purpan - BP 3028 31024 TOULOUSE CEDEX 3 tel: (33) 562 74 45 09 mobile: (33) 608 881481 http://www.u563.toulouse.inserm.fr/