Mr.Kulachat Sae - Jang

Ph.D student in Medical Technology

4436692 MTMT/D

Group 17

Assignment four

Construction of Phylogenetic trees

1.Open www.ncbi.nlm.nih.gov for download DNA sequences.

2.Enter to Entrez and Nucleotide for download DNA sequences from AF408549 AF408562 AF408548 AF408544 AF408543 AF408540 AF408558 AF408557 AF408588 AF408572 AF408571 AF408576 AF408575 AF408568AF408567 AF408566 AF408554 AF408553 and paste it on Ms.word or wordpad.

3.Open www.bionavigator.com

4.You will see bionavigator homepage and input the your login name and password in the dialog boxes and then enter to bionavigator program.

5.Click FILE MANAGER from left menu to construct new file to Workshop.4.

6.Click WORKBENCH from left menu. Then copy first DNA sequences from Ms.word or wordpad and paste on dialog box and click GO>> then save it in originally name such as AF408548 in the Workshop.4. You will see likely below figure and then to do it in the same way again in all DNA sequence respectively.

7.Open RESULTS from left menu to click file which you want to align. In this casts I will select on above file for multiple alignment in ClustalW (fast) program and then run it (Click GO>>). You will see results in the same as below figure.

8.Click down arrow above the page and select in PHYLIP. You will copy the results from phylip format and paste them to Ms.word or wordpad.

9.Open www.cbr.nrc.ca

10.Click SERVICES from left menu and Click WebPhylip.

11.Click Data sampling for paste text file that you copy phylip format from bionavigator to SEQBOOT for bootstrapping and set its for 100 replicates.

12.Select DNADIST in Kimura form for compute DNA distances and set it as YES in USE PREVIOUS DATA SET? and click submit.

13.Select NEIGHBOR- JOINING and set it as YES in USE PREVIOUS DATA SET?.

14.Click Draw cladograms and phenograms or Draw unrooted phylogenies that you want.

15.For reconstruct phylogenic tree. You need download gs700w32 and gsv40w32 for GSview that you can find it in How do I view PostScript files? from left menu.

16.When you download completly then you can see your results in the same as below figures.

16.1 Results from menu Draw cladograms and phenograms.

16.2 Results from menu Draw unrooted phylogenies.