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.
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.
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.
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.
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.
reconcileas an executable. The code for this in the source tar-file, referenced above, and is compiled together with PrIMETV.