Batch processing of beautifying phylogenetic trees I prefer to use treedyn when I decorate many number of phylogenetic trees at one time. In use on Linux desktop, my Perl script works well to convert from raw trees to beautified trees. However, it was stopped at running of treedyn because Tcl of treedyn essentially required a DISPLAY of X-Window when the script was integrated into an Web application. Xvfb (X virtual framebuffer) presents a virtual screen for user or program, which works only on memory not real video device. And xvfb-run.sh , a script of Xvfb, is an utility for command line program. $ xvfb-run.sh my_script.pl -infile tree.phy -outfile tree.ps Please see details of xvfb-run.sh in Dascalita's very concise post . Additional comments Chevenet, the author of treedyn, and Christen recently published ScripTree that is more flexible and functional program for script developers. This ScripTree is also required to use Xvfb in case of backgrou...
Becoming a renaissance man interesting of biocomputing, mechatronics, bioengineering, and culture.