Ks calculation discrepancy (yn00 PAML, MEGA6 nei gojobori)
0
0
Entering edit mode
5.3 years ago
jomaco ▴ 190

The average Ks value calculated for my set of sequences using MEGA6 (Modified Nei-Gojobori (NG96) method with Jukes Cantor correction) was 0.767.

The yn00 result from PAML however works out at 1.56

The results are really quite disparate - what is the reason for this difference, and is this normal?

I have double checked the input files and it all seems to be working correctly, so I have started to look at what a reasonable Ks value might be - I have seen references to sequences with Ks > 1 being unreliable for phylogenetic inference, but have also seen that for ML methods like yn00 some suggestions that Ks < 2 is fine.

This has made be question which result to go with, clearly different tools often give different results, but I would be grateful for your input as without the prior knowledge I am not sure what to go with.

Thanks

yn00 paml ks mega6 nei gojobori • 2.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 1588 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6