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
>
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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