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.
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 background execution without a screen even the program presents built-in CGI interfaces.
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.psPlease 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 background execution without a screen even the program presents built-in CGI interfaces.
References
- F. Chevenet, http://www.treedyn.org/
- Wikipedia, X virtual framebuffer
- D. Dascalita, Building a Flex project with Maven using Hudson on CentOS
- F. Chevenet and R. Christen, http://phylo.lirmm.fr/scriptree/
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