Archaeopteryx configuration

Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. It is available at SBo and is particularly useful if you want to create visually appealing phylogenetic trees, to be used for publication figures or presentation slides. One thing that I do not like is that by default, the program has black interface and black background. I, personally, do not like black themes for my desktop and having a program like this is no exception. Also, I rarely have black slides in my presentations, so I need white background for the trees.

This all can be fixed from the configuration file of Archaeopteryx. It is not included in the generated package, instead it has to be downloaded from the program’s website, in the Download section. here’s a direct link to the example configuration file: _aptx_configuration_file.txt

Download it, modify to your liking and save it in the home folder of your user. The most important change is in the beginning of the file:

#  User Interface Look and Feel
#  ----------------------------
#  Possible values for 'native_ui'
#    'yes' to use native (system) "look and feel"
#    'no'  to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
#    '?'   to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
#          Archaeopteryx-style "look and feel" otherwise

native_ui: yes

The program can draw trees in several cool ways. Combined with the power of Inkscape, different clusters can be highlighted and species indicated to produce a figure such as:

Cool, huh?

Note that the _aptx_configuration_file.txt file does not start with a dot, therefore it is not hidden. I hide it in Thunar, as described here.

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