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DyogenIBENS / Agora

Algorithm For Gene Order Reconstruction in Ancestors
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Agora in living sps #22

Closed DiegoSafian closed 1 year ago

DiegoSafian commented 1 year ago

Hi,

Thanks for this fantastic repo and tools. I am just wondering if Agora can be used with genomes of closely related living sps to reconstruct the genome of their last common ancestors. I do not see why not, but I prefer to ask.

Thanks Diego

alouis72 commented 1 year ago

Hello Diego, I cannot see any problem in using AGORA on genomes of closely related living species . Be aware however that AGORA only reconstructs the order of the ancestral genes and not the ancestral sequences. It is therefore only useful if there are karyotipic differences between your genomes (breakpoints, translation,...). The quality of the reconstruction is also dependent on the number of genomes, the quality of the genomes assembly and annotation, as well as on the quality of the gene trees or families of homologs you will give to the pipeline.

Alex