Can PoMo model be used for SNP data?

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Yiran Zou

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Sep 13, 2019, 9:03:53 AM9/13/19
to IQ-TREE
Hello,

Currently, I am trying to use the PoMo model in IQ-TREE to deal with the heterozygous SNP from the single cell sequencing result of human tumor cells. However, I found that PoMo model does not yet support ascertainment bias correction. Is that means I cannot use the PoMo model to build trees for SNP sites?

Appreciate any reply.

Regards,
Yiran

Minh Bui

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Sep 29, 2019, 4:53:20 AM9/29/19
to iqt...@googlegroups.com, Dominik Schrempf
Dear Yiran,

Dominik should better answer your question. But as far I as remember, this question was already asked and answered in the forum… I don’t have the URL right now, but pls just search for it.

Cheers,
Minh

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Minh Bui

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Sep 29, 2019, 5:08:24 AM9/29/19
to iqt...@googlegroups.com, Yiran Zou
On 13 Sep 2019, at 11:03 pm, Yiran Zou <zoey...@gmail.com> wrote:

Dominik Schrempf

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Sep 30, 2019, 2:28:52 AM9/30/19
to iqt...@googlegroups.com, Yiran Zou
Hello,

yes, the situation has not changed since then. PoMo has to infer the level of
heterozygosity, and so, needs to know the ratio of monomorphic to polymorphic
sites. Is it possible for you to include these sites into your alignment? I
think we could implement ascertainment bias correction into IQ-TREE+PoMo, but it
is a little more involved.

Dominik

Minh Bui <minh...@univie.ac.at> writes:

> Here is the URL to the thread about this:
>
> https://groups.google.com/forum/#!searchin/iqtree/pomo$20ascertainment%7Csort:date/iqtree/xVxurAjvoIY/QayzWsZ_AwAJ <https://groups.google.com/forum/#!searchin/iqtree/pomo$20ascertainment|sort:date/iqtree/xVxurAjvoIY/QayzWsZ_AwAJ>
>
> Minh
>
>> On 13 Sep 2019, at 11:03 pm, Yiran Zou <zoey...@gmail.com> wrote:
>>
>> Hello,
>>
>> Currently, I am trying to use the PoMo model in IQ-TREE to deal with the heterozygous SNP from the single cell sequencing result of human tumor cells. However, I found that PoMo model does not yet support ascertainment bias correction. Is that means I cannot use the PoMo model to build trees for SNP sites?
>>
>> Appreciate any reply.
>>
>> Regards,
>> Yiran
>>
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