The *__combine.txt file format is different from the tutorials. about dsuite HOT 3 CLOSED

Hi Kun

The _combine.txt output changed since Dtrios and DtriosCombine started to also calculate f4-ratios. The first six columns are as before, and six more columns were added with numbers needed for the f4-ratio calculation. We are going to update the tutorial accordingly.

Kind regards
Milan

from dsuite.

Dear millanek,
I am comparing the outputs of Dtrios. The results below :
__tree.txt |
P1 | P2 | P3 | Dstatistic | Z-score | p-value | f4-ratio | BBAA | ABBA | BABA |   |  
Species2 | Species1 | Species3 | 0.154233 | 8.57549 | 4.93E-18 | 0.0300724 | 11495.2 | 1493 | 1094 |  
Dmin.txt |
P1 | P2 | P3 | Dstatistic | Z-score | p-value | f4-ratio | BBAA | ABBA | BABA |   |  
Species2 | Species1 | Species3 | 0.154233 | 8.57549 | 4.93E-18 | 0.0300724 | 11495.2 | 1493 | 1094 |  
_combine.txt |
Species1 | Species2 | Species3 | 11495.2 | 1493 | 1094 | 12886.5 | 3829 | 13482.5 | 13268 | 14225.5 | 3484.5

I am wondering, since in _combine.txt the fifth column correspond to the ABBA and the sixth to the BABA (in bold) and given Species1 | Species2 are inverted compared to Dmin.txt why do the ABBA and BABA sites remain in the same order (see Dmin.txt output )? should not being inverted?

Best regards,

Nicolò Tellini

from dsuite.

An updated detailed tutorial is now available:
https://github.com/millanek/tutorials/tree/master/analysis_of_introgression_with_snp_data

Hope you and others find it helpful
Milan

from dsuite.