perspecies_eventcount and nodes

[Grégoire Michoud]

Hi,

Quick question, I'm not super clear why the nodes values for the perspecies_eventcount files for the "presence" columns are floating values

species_label, speciations, duplications, losses, transfers, presence, origination, copies, singletons

Node_2020_CN_B_W_1_bin.182.purify_2020_CN_DB_w_1_bin.76.purify_0, 1156.77, 4.67, 216.88, 84.99, 869.28, 0.16, 1156.77, 1089.14
Node_2020_CN_N_W_2_0m_bin.145.purify_2020_CN_B_W_1_bin.182.purify_0, 1001.88, 0.65, 271.36, 116.94, 801.5, 0.12, 1001.88, 972.31

Also and related to that, is there a way to find out which gene families are present at a given node?

Thanks Greg

[Benoit Morel]

Hi Grégoire,

I assume that you are using AleRax, not GeneRax

For each family, AleRax samples n (100 by default) reconciliations randomly from the joint distribution. More likely reconciliation scenarios will appear more often than unlikely reconciliations. It then sums the values ( number of gene copies, originations, duplications etc.) over all samples and all gene families, but divides by the number of samples, which is why you get floating values.

There is not one file that will directly list the gene families present in a given species, but for each family, there is a file with per-species event counts, that you could use to determine if the gene family is present or not in this species. 

Maybe you saw it already, but the list of the output files is described here Outputs · BenoitMorel/AleRax Wiki · GitHub 

Hope it helps!

Benoit

Le mer. 26 févr. 2025 à 17:30, Grégoire Michoud <gregoire...@gmail.com> a écrit :

Sorry I meant copies not presence

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