Arginase: A Constant Among Life's Diverse Taxa
Bioinformatics Research Project By:
Austin Lorynski, Kajal Patel, and Laura Ordonez
Phylogenetic Tree
The values depicted on the branches of the phylogenetic tree are bootstrap values. These values were calculated to determine the frequency of similarity of arginase protein sequences among the various organisms represented in the phylogenetic tree. Higher bootstrap values are indicative of a greater degree of similarity between species. Lower bootstrap values are indicative of a lesser degree of similarity between species.
Evolutionary analysis by Maximum Likelihood method
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The evolutionary history was inferred by using the Maximum Likelihood method and JTT matrix-based model [1]. The tree with the highest log likelihood (-4009.15) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the JTT model, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site (next to the branches). This analysis involved 15 amino acid sequences. There were a total of 448 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [2]
1. Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.
2. Kumar S., Stecher G., Li M., Knyaz C., and Tamura K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 35:1547-1549.
3. Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
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