Dear Hyphys,

I have some questions regarding the KH test applied after a GARD run (RecombinationProcessor.bf). Let's do it with some examples:

Gene #1

5 partitions were found by GARD:
- Partition 1: 0-308
- Partition 2: 309-426
- Partition 3: 427-813
- Partition 4: 814-998
- Partition 5: 999-1922

From the RecombinationProcessor.bf output we obtain:

Code:

[...]
KH Testing partition 1
Tree 2 base LRT = 12.8929. p-value = 0.0758
[...]
KH Testing partition 2
Tree 1 base LRT = 49.6799. p-value = 0.0001
Tree 3 base LRT = 8.68062. p-value = 0.0001
[...]
KH Testing partition 3
Tree 2 base LRT = 59.6993. p-value = 0.0001
Tree 4 base LRT = 24.3077. p-value = 0.0001
[...]
KH Testing partition 4
Tree 3 base LRT = 16.3848. p-value = 0.0001
Tree 5 base LRT = 62.1624. p-value = 0.0001
[...]
KH Testing partition 5
Tree 4 base LRT = 10.3781. p-value = 0.0001
A total of 3/4 significant couplings
Mean splits identify: 0.165
 

Gene #2

2 partitions:
- 0-807
- 808-1013

RecombinationProcessor.bf output:

Code:

[...]
KH Testing partition 1
Tree 2 base LRT = 23.8159. p-value = 0.1265
[...]
KH Testing partition 2
Tree 1 base LRT = 104.634. p-value = 0.0001
A total of 0/1 significant couplings
Mean splits identify: 0.25
 

So, with the first gene, all the test are significant (at the 0.05 level), except when we fit the topology of the partition 2 on the partition 1. Basically, partition 1 has not a significantly different history than partition 2, but partition 2 has one.  ???

The same is observed with the gene #2.

In those case what should we do? Considered that if 2 is significantly different than 1, that implies that 1 is different than 2, and that the test was not significant because of a lack of power (e.g. small partition)?

By the way, what does the "A total of x/x significant couplings" and "Mean splits identify: xxx" mean?

Thank you,
-Tristan

Thank you Sergei,
So just to be sure I follow you, for gene #1 you only consider 4 partitions (1+2, 3, 4, 5), and for gene #2, you conclude that there is no evidence of recombination, correct?


-Tristan