Darwinbots Forum

Bots and Simulations => Evolution and Internet Sharing Sims => Topic started by: Sprotiel on January 19, 2007, 09:03:09 PM

Title: Phylogenetic trees from sim files
Post by: Sprotiel on January 19, 2007, 09:03:09 PM

I've created a small Python script to analyse mutation histories in saved simulation files. What it does is building a phylogenetic tree from the mutation details (taking advantage of their being saved in plain text). There must be some useful things to do with this, but I only print the tree with the numbers of bots having a particular genome, or having it as an ancestor.

Limitations : it ignores bots that never mutated, may give nonsensical results if you've ever stripped mutation details or if you have more than one species mutating.

To use it, you need to have Python installed. If you know some Python, I hope you'll figure out what it does, otherwise, I'm also including a handy batch file on which you can drag and drop .sim files.

Title: Phylogenetic trees from sim files
Post by: Numsgil on January 20, 2007, 12:45:43 AM

Neat.  I'll try to install Python and test it later.

Title: Phylogenetic trees from sim files
Post by: scood on February 18, 2007, 11:21:18 PM

wow this sounds cool, imagine if you have spiecation, then this would show really dyynamic phylogenic trees forming.

now can you plz explain how to use it?
cause I cant figure it out

Title: Phylogenetic trees from sim files
Post by: scood on April 08, 2007, 02:06:22 PM

someone PLEASE TELL ME how to use it I dont know how to use it

Title: Phylogenetic trees from sim files
Post by: Numsgil on April 09, 2007, 07:15:51 PM

It's a python script.  You'll need to install python on your computer.  Sprotiel has it installed to the root C drive (ie: c:\Python25).  This is fairly common with this sort of programming utility.  Setting up python is beyond the scope of my post, but you should be able to figure it out if you start here (http://www.python.org/).

Once you have python installed, you'll need to unzip his utility to your Darwinbots folder.  Then, drag and drop a sim file onto the .bat file included, and it should run.  Otherwise, you can edit the python file to run your sim.

Title: Phylogenetic trees from sim files
Post by: scood on May 27, 2007, 06:55:16 PM

im  still confuzzled


I did what you said and it didn't draw a tree

Title: Phylogenetic trees from sim files
Post by: scood on May 27, 2007, 07:00:14 PM

it says attribute error

Title: Phylogenetic trees from sim files
Post by: Numsgil on May 28, 2007, 01:10:51 AM

How far in the process did you get?  Did you get python successfully installed?