Understanding the grapetree distance computation

[crarlus]

Hi,
I have some doubts whether I understand the "--missing" option in the CLI grapetree version correctly. This is what it says in the help file:

  --missing HANDLER, -y HANDLER
                        ONLY FOR symmetric DISTANCE MATRIX.
                        0: [DEFAULT] ignore missing data in pairwise comparison.
                        1: Remove column with missing data.
                        2: treat data as an allele.
                        3: Absolute number of allelic differences.

I ran the distance calculation for some allele profiles, and when I check the resulting distances and compare it to a custom distance script, I think that --missing 3 gives me actually something like "ignore missing data in pairwise comparison".

Could you please clarify:

• What do you mean by "Absolute number of allelic differences"? In earlier versions this case was termed "Naive counting of absolute differences between profiles"?
• How are "-" entries treated in this case (--missing 3)?
• And how are the differences computed for --missing 0

Also I noticed that the resulting minimum spanning trees MSTreev2 contain the distances according to --missing 3?

Thanks for your help?

[zheminzhou]

For --missing 0, the differences are calculated as:
(Number of different alleles)/(Number of loci that present in both genomes)*(Total number of loci)

For --missing 3, missing loci are ignored and only the real different alleles are counted.
A: 111
B: 12-
Will have a distance of 1.

"Also I noticed that the resulting minimum spanning trees MSTreev2 contain the distances according to --missing 3?“

Yes, for easy interpretation of the results, the branch lengths of the MSTreeV2 result is re-calculated using "--missing 3".