Quick question about the results of the output family_opx_osci_perspecies_eventcount.txt in AleRax

[Benjy Luis Sedano-Herrera]

Hi,

I hope you are doing well,

 I have ran AleRax with only one protein family (OPX) containing mutiple copies per species.  I just wanted to ask about this output (family_opx_osci_perspecies_eventcount.txt) in AleRax

-Does this ouput represent the number of events of gene duplication, losses and transfers? Or is the rate of gene duplication, losses and transfers?

-Does the column called "speciations" represent the number of gene copy numbers in each special label and the number of ancestral gene copy numbers on the internal nodes?

Thank you so much in advance for your help and time.

Please find attached the file.

Best,

Benjy Sedano-Herrera

[Benoit Morel]

Hello,

- That's the number of events. Since AleRax samples the reconciliations several times, the number is averaged over the samples and might sometimes not be an integer number. But it's not a rate.

- You're correct

I hope that helps

Benoit

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