This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.

DNA Phylogeny

The tree shown below were produced by program Phylogeny.fr [1] using protein FASTA sequences of KRAS DNA homologues obtained from Homologene [2]. Each tree was generated using different construction parameters. Phylogeny.fr allows one to determine the phylogenetic tree using the FASTA format of genes and proteins. Even though much of the DNA sequence had to be truncated so that it can be analyzed by Phylogeny.fr, the tree generated by it appears to be fairly accurate (in contrast to the alignment analysis by T-Coffee using truncated FASTA DNA sequences, which did not make sense).

TreeFam Phylogenetic Tree

The above tree was obtained from TreeFam[3]

Analysis

The phylogenetic tree obtained using the program Phylogeny.fr[1] and the one from TreeFam is highly similar, indicating the likelihood of the results being accurate. Expectedly, Chimpanzees and humans are the closest in the phylogenetic tree as chimps share up to 98% of human DNA. C.elegens being further from all the mammals is also an expected result, since, as an invertebrate, it's evolution probably diverged long ago from mammals. Interestingly, truncating FASTA DNA sequences in Phylogeny.fr produced expected results in contrast to alignment analysis using T-coffee. 

References

1) Phylogeny.fr
http://www.phylogeny.fr/
2) Homoleogene
http://www.ncbi.nlm.nih.gov/homologene
2) TreeFam
http://www.treefam.org