If you use PrIMETV, please cite:
Sennblad B et al (2007) primetv: a viewer for reconciled trees. BMC Bioinformatics 8, 148
PrIMETV: A PrIME Tree Viewer
PrIMETV is a program that can visualize tree-within-tree phenomena
such as gene/species tree
reconciliations.
Output can be given in a range of formats, e.g. PostScript, Fig, and SVG.
Thus, it is possible to easily edit the final illustration in
many available drawing programs. PrIMETV can also directly
manipulate important attributes such as color and layout policy.
You can try out PrIMETV on the webb too. Our web service,
reduced the need to download and install the actual application.
Click an image for a high
resolution PDF.
Two distinct reconciliations for the same fictional gene tree.
A reconciled phylogeny for the Major Histocompatibility
Complex class I for three primates.
A biogeography illustration: The species evolution of Southern
Beech, nothofagus, is reconciled to a hypothetical
continental break-up tree.
Two distinct reconciliations for the same fictional gene tree.
A reconciled phylogeny for the Major Histocompatibility
Complex class I for three primates.
A biogeography illustration: The species evolution of Southern
Beech, nothofagus, is reconciled to a hypothetical
continental break-up tree.
A manual describing PrIMETV and the accompanying reconciliation
program RECONCILE, plus the file formats used, is available as a
PDF file.
FAQ
- Why does not my the tree arcs show up when I view a PDF
file on my Mac?
This is due to a setting in Mac OS X Preview. Go to the "PDF" tab in Settings and uncheck the option for anti-aliasing.
Another workaround is to use Adobe Reader.
- Why does the text not show up when I view a PostScript (PS) file (or PDF converted from PS) on my Mac?
First of all, if you compile PrIMETV yourself, please make sure to use our patched version of plotutils!
As a workaround, you can also open the PS file in another program, such as Adobe Illustrator. The behaviour is due to an incompatibility between plotutils and pstopdf.
Release 1.5.6:
Removed a compilation errors, due to bitrot.
This is distributed under the GNU General Public License. You also need the GNU Plotutils, and we recommend our slightly edited version. We have compiled and used this on Red Hat Linux (version 9), the Red Hat-derived CentOS, and Microsoft Windows (cygwin 1.5.18-1). On Mac OS X, this seems to work as-is in Darwin Ports.
Old releases
Release 1.5.5:
Removed some warnings and compilation errors appearing in Bison 2.4 and GCC 4.3.2.
Release 1.5.4: More intelligent handling of lack of branchlength on species tree's root node. Thanks, Minh Anh Nguyen.
Release 1.5.3: Compilation fixes, improved installation instructions.
Release 1.5.2: Layout fixes, now including readReconciliation.
Release 1.4: bug and layout fixes, can now rotate nodes in guest tree to avoid unnecessary line crosses.
Release 1.2: fixes small bug in reading trees.
Binaries
An
executable
and
an accompanying library
for the drawing. It works on Red Hat Linux version 9
(Shrike) and CentOS. We have not been able to do static linking with GNU Plotutils, so you have to put the library in the load-path. An alternative is to put the library in its own location and make sure that LD_LIBRARY_PATH includes this path.
Reconciliation tool
The reconciliation tool reconcile as an
executable. The code for this in the
source tar-file, referenced above, and is compiled together
with PrIMETV.
readReconciliation
With readReconciliation (executable here), you convert a reconciliation on a tabular format (easy to edit), to the tree format that PrIMETV uses.
Patient users have helped us improve PrIMETV: Thank you from the
PrIMETV team!
- Abhiman Saraswathi
- Robert Karn
- Christina Laukaitis