I attached a few documents that should be helpful in understanding my presentation about using AvidaEd in conjunction with phylogenetics programs.
Helpful formatting notes for using AvidaEd and phylogenetics –> this file details each step of isolating Avida individuals, translating their genomes, and inputting them into the phylogeny site.
Also, the free download of AvidaEd is available here: http://avida-ed.msu.edu/
I used this link for to convert the genomes from excel into a FASTA format: http://genome.nci.nih.gov/tools/reformat.html
And finally, here is the link to the phylogentics site I used: http://www.phylogeny.fr/version2_cgi/index.cgi
final generation gene sequences FASTA –> Here are some genomes already converted into the FASTA format in case you wanted to play around using the phylogeny site! I would encourage playing around with the different settings on this site; some methods may produce more accurate phylogenies!
I hope that my presentation was helpful and encourages new uses of AvidaEd technology in the classroom. While there are some minor formatting and computing skills necessary for using these programs, I think that it is a really awesome application and example of Evolution and Phylogentics. Please feel free to contact me at firstname.lastname@example.org if you have any questions about my project or how to use these programs!