Home page for the phylodirector program in the DART package.
The following page describes the phylodirector program for visualizing transducer state paths as animations.
How to obtain phylodirector
- Install the Berkeley Mpeg Encoder and the GD Perl module
- Ensure GD.pm is in your PERL5LIB and mpeg_encode is in your PATH
- Download the DART package (see Downloading Dart)
- Add the dart/perl directory to both your PERL5LIB and PATH environment variables
- Try running the phylodirector.pl script, which should now be in your PATH.
This diagram is a key to the icons for the various state types of the branch transducers:
Note that these icons are slightly different from those in the graphviz figures elsewhere on this wiki. Different icons; same formalism.
How to read this document
What, impatient? Skip to the Example Movies.
Theory: string transducers
For discussion of the theoretical framework of finite-state transducers, see one of the following pages:
- Phylo Composer (manual for software tool, gives concrete examples);
- String Transducers (brief overview, with lots of links).
The general usage is
phylodirector.pl [options] [[Alignment File]]
The program can also be used as a Unix filter:
cat [[Alignment File]] | phylodirector.pl [options]
For a full list of options, type phylodirector.pl --help.
The primary output is an MPEG format movie.
Example input files
Nanos translational control element
This file, nos_TCE.stock, generates a 16Mb movie in approx 6 minutes on a 1.5GHz Apple PowerPC laptop with 1.25Mb RAM.
The output is linked below.
The Phylo Film page has downloadable examples of transducer animations generated using phylodirector, as well as lots of other animations e.g. forward-time simulations of indel models.
Here's a somewhat clunky YouTube:
<object width="425" height="350"> <param name="movie" value="http://www.youtube.com/v/EcLj5MSDPyM"> </param> <embed src="http://www.youtube.com/v/EcLj5MSDPyM" type="application/x-shockwave-flash" width="425" height="350"> </embed> </object>
Here's another YouTube, this time of the above nanos TCE example:
<object width="425" height="350"> <param name="movie" value="http://www.youtube.com/v/LhezqZ186uI"> </param> <embed src="http://www.youtube.com/v/LhezqZ186uI" type="application/x-shockwave-flash" width="425" height="350"> </embed> </object>
-- Ian Holmes - 18 May 2007