Phylogenetic+Tree+(VCFS-TBX1)

To study genetic diseases, a model organisms are usually used. Model organisms provide valuable data in analyzing human development, gene regulation and evolutionary process. Model organisms includes mammals, non mammals, and other organisms [6]. Mammal models includes: Non mammals includes:
 * Mouse
 * Rat [6].
 * Archaea
 * Microbes
 * Fruit fly (//Drosophila melanogaster//)
 * Mosquitoes
 * Round worm (//Caenorhabditis elegans//)
 * Retroviruses
 * Yeast (//Saccharomyces cerevisiae//)
 * Zebra fish (//Danio rerio//)
 * Amoeba (//Dictyostelium discoideum//) [6].

Other organism includes:
 * Flowering plant (//Arabidopsis thaliana//) [6].

These organisms helped scientists and researchers in finding cures for those genetic diseases and understand human development without using human models. They are used because they are small in size, easy to grow, cheap, reliable, and has short life cycle [6]. To be able to determine which model organism is suitable to study for a specific genetic disease, a phylogenetic tree is used. The phylogenetic tree is a branching diagram showing the evolutionary relationships of different species based on its physical and/or genetic similarities and differences. Geneious database is the database were the sequences of TBX1 was taken. The sequences used were the following:
 * Olive baboon (//Papio anubis//) - TBX1- 101020954
 * Dog (//Canis lupus familiaris//) - TBX1 - 608214
 * Chimpanzee (//Pan troglodytes//) - TBX1 - 458653
 * Norway rat (//Rattus norvegicus//) - Tbx1 - 360737
 * House mouse (//Mus musculus//) - Tbx1 - 21380
 * Human (//Homo sapiens//) - TBX1 - 6899

These sequences were imported to Mega database to be able to align the sequences using the ClustalW alignment with the following parameters: //For both Pairwise and Multiple Alignment; Gap Opening Penalty: __15__; Gap Extension Penalty: __6.66__; DNA Weight Matrix: __IUB__; Transition Weight: __0.5__; Use Negative Matrix: __OFF__; Delay Divergent Cutoff (%): __30__.//

The same Mega database was used to generate phylogenetic tree using the default parameters as following: //Analysis: __Phylogeny Reconstruction__; Statistical Method: __Maximum Likelihood__; Test of Phylogeny: __Bootstrap Method__; No. of Bootstrap Replications: __500__; Substitution Type: __Nucleotide__; Model/Method: __Tamura - Nei Model__; Rates Among Sites: __Uniform Rates__; Gaps/Missing Data Treatment: __Completion Deletion__; Selection Codon Positions: __1st, 2nd, 3rd, and Noncoding Sites__; ML Heuristic Method: __Nearest-Neighbor-Interchange (NNI);__ Initial Tree For ML: __Make initial tree automatically (Default-NJ-BioNJ);__ Branch Swap Filter: __Very Strong__; Number of Threads: __1__.//

To study the TBX1 gene, the chimpanzee (//P//. //troglodytes//) will be the best model to use. As seen in the figure below, human (//H. sapiens//) and chimpanzee (//P. troglodytes//) have a bootstrap number of 96, which means that chimpanzee has similar TBX1 gene to human TBX1 gene. Olive baboon (//P. anubis//) have also the similar gene, but not quite similar as compared to the chimpanzee. However,the TBX1 gene of Norway rat (//R. norvegicus//) is not similar to human gene, as seen in the figure below, there is no bootstrap value for Norway rat.

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