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DyogenIBENS / Agora

Algorithm For Gene Order Reconstruction in Ancestors
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Too many contiguous ancestral regions (CARs) #14

Closed kuangzhuoran closed 1 year ago

kuangzhuoran commented 2 years ago

Hi ! I got 260 CARs and I have used agora-plants.py and agora-vertebrates.py. And I used orthoGroups as input ( The genus I studied has only eight species...

Is it because the number of species is too low, and is there anything I can do to improve this result?

DyogenIBENS commented 1 year ago

Hello, it is not the number of CARs that is important but the distribution of the CARs's size. You can have 260 CARS but only 15 with size > to 20 genes and a lot of very little ones. Which can lead to what we call a Chromosomal reconstruction if descendant genomes have ~15 chromosomes. Also, the reconstruction will depend on the number of genomes you have (descendants and outgroups), the quality of assembly for each genome, the conservation in gene organisation between these genomes, the quality of annotations for each species and the relevancy of OrthoGroups (depending of the methodology used to compute them). It's difficult to say why you have 260 CARs and if it is a problem without knowing what species you're analyzing. Unfortunately, as I don't have any clue on the data, it's hard for me to orient you on what you should expect. Don't hesitate if you have any other question. regards, Alexandra