Dear all

I am working on a large data set(N500-l11000) of 10 protein coding genes. i feel that some lineages in my data are deviating from molecular clock assumption. but i don't know how to find those particular lineages.

for example
I have 20 branches in a tree out of 20 i feel 4 branches have different evolutionary rates. But i don't what are those branches whether it could be possible to identify those branches.

since i am new to this sort of analysis please let me know in simple terms.

Dear Raja,

Perhaps the easiest thing to start with is to test for the presence of a global molecular clock in your data. This test is implemented as a standard analysis in HyPhy (under the Molecular Clock rubrik), and it will tell you whether or not a molecular clock model can be rejected for the entire tree.

However, this test will not tell you which branches are responsible for the deviations. You could try the local molecular clock analysis (also implemented in HyPhy) to see which complete subtrees are clocklike and which are not to help pinpoint the source of the deviation.

Is it important for you to know the actual branches, or just that the clock has been violated?

Best,
Sergei

Thank you very much.
I fell i need to do local molecular clock to get the nodes which are deviating.
I feel i will be able to do this. since my data set is large it mat take some time. when it completes i will get back.