perspecies_eventcount.txt and ancestral genome size

[Saioa Manzano]

Hi Benoit,

I'm having issue understanding the columns on the output perspecies_eventcount.txt. If I understand correctly, this is the sum of all FAM_perspecies_eventcount.txt which in turn is the average of all the samples per FAM. 

Then, "presence" would be the number of FAMs present in that given node, so to obtain the genome size (number of genes) in a given node i would have to calculate speciations + duplications - losses + transfers + origination, no?

[Benoit Morel]

Hi Saioa,

Sorry for the late reply, I have left academia and have less time to support the tools

We always used the convention that we count the number of copies at the moment where the species is split into two new species. For that you need to count both the S and SL events (speciations and speciations for which one of the two lineages has been lost). Note that we miss the copies that were lost in both lineages, but since we can't observe them, this number is impossible to quantify.

I would never count the duplicaitons, transfers and originations. 

Examples:

- if an origination occurs in branch E, and if this gene copy survives until the branch E is split into two new branches, you will observe one origination and one speciation. But there is one single copy, and it is counted by the speciation.

- if there is one single copy at the very beginning of a branch F, and a gene is duplicated in the same branch, you will observe one duplication and two speciations (because each gene copy reaches the speciation node and is passed to both children of F). The number of copies is 1 at the begining of the branch, 2 at the end, but never 3 (which is the number you would get if you count duplications and speciations)

Let me know if that makes sense, it's a bit tricky to explain without drawing :)

Benoit

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