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popgenmethods / SINGER

Sampling and inference of genealogies with recombination
MIT License
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multiple trees sequences generated #18

Closed mehakmadhura closed 4 months ago

mehakmadhura commented 4 months ago

Hello! It would be great if you could explain why the program generates multiple tree sequence files and why the number of trees sequences generated equals the number of samples. Thanks!

YunDeng98 commented 4 months ago

Hi @mehakmadhura SINGER is a Bayesian method which draws samples from the posterior distribution, so that is the reason why there are multiple tree sequences returned by the program. The number of samples is default at 100 but you can set it using the -n flag.

mehakmadhura commented 4 months ago

thank you so much. Also, I am a bit confused about the -Ne argument required by the software. Is it fine to calculate the Ne from pi for a rough estimate? Wouldn't population structure affect it, for example?

YunDeng98 commented 4 months ago

@mehakmadhura the Ne argument only needs to be rough estimate. Also, the most recent version 0.1.8 gets rid of the -Ne argument.

mehakmadhura commented 4 months ago

Thank you!