Home page for the
program in the
The following page describes the
for visualizing transducer state paths as animations.
How to obtain phylodirector
Install the BerkeleyMpegEncoder and the GD Perl module
is in your
is in your
PATH Download the DART package (see DownloadingDart)
directory to both your
PATH Try running the
script, which should now be in your
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
elsewhere on this wiki.
Different icons; same formalism.
How to read this document
What, impatient? Skip to the
Theory: string transducers
For discussion of the theoretical framework of finite-state transducers, see one of the following pages:
The general usage is
phylodirector.pl [options] AlignmentFile
The program can also be used as a Unix filter:
cat AlignmentFile | phylodirector.pl [options]
For a full list of options, type
The input file should be in
and should use the ability of that format to associate a
tree with a multiple sequence alignment.
The primary output is an
Still images are output in
Example input files
Nanos translational control element
generates a 16Mb movie in approx 6 minutes
on a 1.5GHz Apple PowerPC laptop with 1.25Mb RAM.
The output is linked
page has downloadable examples of transducer animations generated using
as well as lots of other animations e.g. forward-time simulations of indel models.
Here's a cartoon of a multi-sequence transducer in action:
Evolutionary HMM (Quicktime)
Evolutionary HMM (AVI)
Evolutionary HMM (MPG) and here is a legend for the EHMM movies (PDF)
Here's a somewhat clunky YouTube:
Here's another YouTube, this time of the above
- 18 May 2007