In order to calculate Ka/Ks, first you have to align your sequence. One of the advantages of Mega5.0 is that it is multifunctional and can be used in many bioinformatics analyses such as phylogenetic study. Therefore, a built-in alignment tool, ClustalW, is incorporated into Mega5.0 to align multiple sequences.
In this tutorial, we only focus on the application of Mega5.0 in positive selection, which calculates the ratio of Ka/Ks in target sequences.
In this tutorial, we only focus on the application of Mega5.0 in positive selection, which calculates the ratio of Ka/Ks in target sequences.
Steps to calculate Ka/Ks:
1. Open Mega5.0àAlignàEdit/Build align
2. Copy & paste your sequencesà AlignmentàAlign by ClustalW
3. DataàExport Alignmentà Mega format (save for future use)
5. Go back to the main interface: DistanceàCompute pairwise distances
6. Now a new window shows up, and you can select different models in Substitution Model, and either Ka or Ks in the Substitutions to include
7. This table gives you the Ka, if you choose ‘Nonsynonymous only’
8. To get overall value of Ka, choose AverageàOverall
9. You can export this table as excel by clicking the ‘Export’ option in File and select XL as output format
10. You need to repeat step 6 but to choose ‘Synonymous only’ to get Ks.
11. Divide Ka by Ks and get Ka/Ks ratio.
Hi.. all your tutorials are simple and great. Could you show the the process of calculating dn ds in paml package, mainly the branchsite tests and the codeml models??
ReplyDeletei am looking for the the same analysis. did you have any luck
Deleteif you use Align by ClustalW (codon), the data would be quite different from that from Align by ClustalW. Which one should be better?
ReplyDelete