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bcm-uga / Loter

A software package for local ancestry inference and haplotype phasing
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help for chloroplast genomes #8

Closed Mirror361025 closed 5 years ago

Mirror361025 commented 5 years ago

Hi. I am Eda. Recently, I wanna detect the heteroplasmy and Infer Local Ancestry among 16 populations of 27 different species based on cp genomes. Could I use Loter to conduct these analyses for chloroplast genomes????

Mirror361025 commented 5 years ago

or it just can be used for nuclear genomes?

gdurif commented 5 years ago

I am not familiar with the specificity of chloroplast genomes, however if you have haplotypes data (0-1 SNP tables) for admixed individuals and for individuals from different reference population, I don't see why Loter would not work.

Indeed, our method is purely computational (least square criterion with a penalty on the jump form a reference to another) and does not implement any specific biological assumptions.

mblumuga commented 5 years ago

or it just can be used for nuclear genomes?

No, it handles haplotypic data and cp genomes should be fine. Even with diploid data, loter expects phased haplotypes.

Mirror361025 commented 5 years ago

thanks