1. T.Y.BSc SEMESTER V BOTANY PAPER III UNIT III BAR CODING
By Mrs. S. S.HAJIRNIS
DEPARTMENT OF BOTANY
SATISH PRADHAN DNYANASADHANA COLLEGE,THANE(W)

2. BAR CODING
MEGA 6.Exec.

3. dendro 5 proper sequence. FAS
File - Mega 6. Exec
file session
Click open
Go to (wherever) the folder is stored e.g. Desktop
Click ok
dendro 5 proper sequence. FAS
Go to Analyze
Nucleotide
ANALYSE

4. Protein coding nucleotide sequence data
Click Ok
Protein coding nucleotide sequence data
Select Genetic Code
Standard
Click TA
Species aligned
C (conserved sites) TA

5. Compute pairwise Distance
Click
V -----(Variable sites)
Pi-----(Parsim-info sites)
Minimise the active window
Go to task bar
Distance
Compute pairwise Distance
click

6. Reuse currently active data Kimura 2-parameter model
Click
Analysis Preference
Kimura 2-parameter model
Compute
click
Data obtained

7. Convert data into excel sheet Go to file Click Export print distance
XL Microsoft Excel Workbook
Print Save Matrix
Open Excel File
Select
Conditional Formatting

8. Format only Top and Bottom Ranked Values
Select column B-E
Top / Bottom Rules
Click
More rules
New formatting rules
Format only Top and Bottom Ranked Values
Format
Fill colour (preferably a light colour) ok
Top (only 1 value)

9. Format only Top and Bottom Ranked Values Bottom (only 1 value) Format
In excel file
Go to
Top / Bottom Rules
Click
More rules
New formatting rules
Format only Top and Bottom Ranked Values
Bottom (only 1 value)
Format Ok
Top most value Highlighted
Go to
Select column B-E with all values

10. Fill colour (preferably a light colour) Ok Lowest value highlighted
Use formula to find out the % species identification
Total no. of species – no of species with zero distance × 100
Total no. of species

11. Phylogenetic Tree

12. Construct / Test Neighbour joining Tree
Minimise the Excel Sheet
Go to
MEGA 6. exe.
Phylogeny
Click
Construct / Test Neighbour joining Tree
Use currently active data
Analysis Preferences
Test of Phylogeny

13. Phylogeny tree obtained
Boot Strap Method (loop) check the similarities between the sequences 1000 times
Enter instead of 500
Compute
Phylogeny tree obtained
% significance can be checked
Take a print out of the result obtained

14. THANK YOU……..