What is the difference between ploidy types "mitochondrial" & "Y" in BEAST 1 EBSP?

Pavel Rinkman

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Aug 2, 2022, 11:34:29 AM8/2/22

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Hello, everyone!

I am analysing a virus phylogeography, & would like to try EBSP population model (I have hitherto used SkyGrid). There is an option to choose ploidy type. I cannot understand the difference between mitochondial & Y ones? What should I prefer, for instance, for Hepatitis A virus? I thought that ploidy type is just gene copy factor, & they are equal for Y-chromosome & mitochondrial DNA, aren't they?

Best wishes,

Pavel

Artem B

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Aug 5, 2022, 2:13:58 AM8/5/22

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Hello Pavel
It seems to be the same things:
"Ploidy (copy number) for the gene, typically a whole number or half (default is 1) autosomal nuclear: 2, X: 1.5, Y: 0.5, most viral: 1, mitrochondrial: 0.5"
https://www.beast2.org/2022/05/01/bicpes-tree-prior.html

Best,
Artem

вторник, 2 августа 2022 г. в 23:34:29 UTC+8, Pavel Rinkman:

Pavel Rinkman

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Aug 5, 2022, 4:10:43 AM8/5/22

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Hello, Artem!

I already noticed this in xml. This is strange that there is no option for viral or bacterial genes.

Best,
Pavel

пятница, 5 августа 2022 г. в 09:13:58 UTC+3, ui.ar...@gmail.com:

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