Phylo Director

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Home page for the phylodirector program in the DART package.

Introduction

The following page describes the phylodirector program for visualizing transducer state paths as animations.

How to obtain phylodirector

  1. Install the Berkeley Mpeg Encoder and the GD Perl module
  2. Ensure GD.pm is in your PERL5LIB and mpeg_encode is in your PATH
  3. Download the DART package (see Downloading Dart)
  4. Add the dart/perl directory to both your PERL5LIB and PATH environment variables
  5. Try running the phylodirector.pl script, which should now be in your PATH.

Visual legend

This diagram is a key to the icons for the various state types of the branch transducers:

File:PhyloDirector.statetypes.png

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

Straight through.

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:

Command-line usage

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.

File formats

Input format

The input file should be in Stockholm format, and should use the ability of that format to associate a Newick format tree with a multiple sequence alignment.

Output format

The primary output is an MPEG format movie.

Still images are output in PNG format or SVG format.

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.

Example movies

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 cartoon of a multi-sequence transducer in action: </em>Evolutionary HMM (Quicktime), Evolutionary HMM (AVI), Evolutionary HMM (MPG) and here is a legend for the EHMM movies (PDF) </p>

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