6. Find the most relevant nucleotide sequence from database. I prefer to ch oose mitochondrial D-loop hypervariable region I to further multiple alignment and phylogenetic tree analysis.
7. After clicking the sequence, the web page displays as shown in the figure. You can select among various types of format such as FASTA, Genbank, and XML. I prefer to use FASTA format and save to notepad program.
8. Open the NCBI web page again. Type “mitochondrial D-loop hypervariable region I human” in the search box.
10. Try to find more relevant sequence, I go to next page as shown in the figure, and choose sequence in the red oval mark.
11. After clicking the sequence, the web page displays as shown in the figure. You can select among various types of format such as FASTA, Genbank, and XML. I prefer to use FASTA format and save to notepad program.
14. After clicking the sequence, the web page displays as shown in the figure. You can select among various types of format such as FASTA, Genbank, and XML. I prefer to use FASTA format and save to notepad program.
17. After clicking the sequence, the web page displays as shown in the figure. You can select among various types of format such as FASTA, Genbank, and XML. I prefer to use FASTA format and save to notepad program.
20. After clicking the sequence, the web page displays as shown in the figure. You can select among various types of format such as FASTA, Genbank, and XML. I prefer to use FASTA format and save to notepad program.
23. After clicking the sequence, the web page displays as shown in the figure. You can select among various types of format such as FASTA, Genbank, and XML. I prefer to use FASTA format and save to notepad program.
26. After clicking the sequence, the web page displays as shown in the figure. You can select among various types of format such as FASTA, Genbank, and XML. I prefer to use FASTA format and save to notepad program.
27. These are whole FASTA formats from NCBI database including human, Neanderthal, chimpanzee, gorilla, orangutan, siamang, and bonobo.
32. Upload the file(al.txt) from computer, and then click the run butoon to let the clustalw execute
33. This figure represents the result from clustalW, and you can save result to the computer by right clicking the file and selecting “save target as”. It automatically downloads to your PC or laptop . Right-click
34. This figure presents result files from ClustalW. alignment file guide tree file output file
41. After Clicking win32, the popup window display as in the figure. Then select save to disk to start downloading the program.
42. After downloading completely, treev32 file appears on the desktop. This figure shows after opening file with the winrar program. Then, double-click the setup file to install the program.
43. The installshield wizard appears on desktop automaically after doule-clicking the setup file.Then, click the next button untill fisnishing the installation process.
50. After click the first website, the home page shows as in the picture. Then click the area that is in red oval shape.
51. The Popup window shows on screen after clicking the “Bioedit.zip”. Select “save to disk” to download to the computer.
52. Use the winrar program to open the file and double-click the setup file to start installing the program . After downloading completely, you get the bioedit file.
53. The installshield wizard show on desktop automaically after doule-clicking the setup file.Then, click the next button untill fisnishing the installation process.
54. After completing install program, press start tab, click all programs and choose the the bioedit to lauach the program.
55. After clicking the biodeit, the program’s graphic user interface shows as in the figure. Open the previous aligment file from clustalW.
56. This figure shows the alignment result . Go to file menu and select save as.
57. Save the file to computer My file is mDNA.phy file. The mDNA file appears on the desktop.
58. Creating tree by Phylip Open the website “google.co.th” and type “phylip” in the search box.
80. Double click the consense program. This program requires intree created by the neighbor program. Consense tree
81. Key letter “ y” and press enter to start the program. After finishing the concense program, you get the outfile and outtre files .
82. Open the outtree file created by the consense program with the treeview software.
83. This figure shows all kinds of phylogenetic tree. radial tree cladogram rectangular cladogram phylogram
84. You can save entire phylogenetic trees to the computer by going to fie menu and choosing save as graphic. After saving completely, all files appear on the desktop.