This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Phylogeny
Phylogeny.fr phylogenetic tree
The figure below shows the phylogenetic tree that was obtained using the "One-click mode" on the program Phylogeny.fr. This particular mode allows the software to make decisions on your behalf based on the set of sequences submitted, optimizing the results for your data. The Homo sapiens HLA-DQA1 gene alignment was compared with the homologous gene in Pan troglodytes (chimpanzee), Canis lupus familiaris (domestic dog), Mus musculus (mouse), and Rattus norvegicus (rat). This tree suggests the chimp HLA-DQA1 gene is most closely related to the Human HLA-DQA1 gene. The mouse and rat HLA-DQA1 genes are the most distant from the Human HLA-DQA1 gene.
GeneBee phylogenetic tree using MUSCLE alignment
The phylogenetic tree produced by GeneBee below produced very different results. The dog HLA-DQA1 was most related to the chimp HLA-DQA1, the rat HLA-DQA1 was most related to the mouse HLA-DQA1, and the human HLA-DQA1 was the most distant from the rest of the homologous organisms. Because MUSCLE was the only program that produced an alignment, there are no other GeneBee phylogenetic trees to compare to.
References
- Phylogeny.fr: http://www.phylogeny.fr/
- GeneBee: http://www.genebee.msu.su/genebee.html
