Crohn's+MEGA

The program MEGA 5 Beta is used for conducting sequence alignments, making phylogenetic trees, and exploring evolutionary theories. MEGA was used in this instance to create a phylogenetic tree to see how closely related the PTPRS gene is in relation to the species aligned in Geneious.



Figure. Molecular Phylogenetic anaylsis by Maximum Likelihood method

The evolutionary history was inferred by using the Maximum Likelihood method based on the JTT matrix-based model [1]. The tree with the highest log likelihood (-8875.4614) is shown. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was < 100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 6 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 1637 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [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. Tamura K., Dudley J., Nei M., and Kumar S. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24:1596-1599.

[|Access to MEGA]

Back to Homepage