Not sure which tool to use for genomic comparison- any suggestions?

Hello, I am relatively new to Galaxy and computational genomics in general but I am trying to complete an undergraduate research project and any help would be greatly appreciated!!

I have a whole bunch (~15) fungus genomes belonging to either group A or group B. I want to see if the group A fungi have any genes that have significantly more copies compared to group B. (basically seeing if group A have higher expression of any genes which could influence their phenotype)

Let me know if there are any tools in Galaxy to do this type of comparison, I have tried using “Gecko” but I did not get any clear output.

Thank you!, Any feedback is greatly appreciated

Hi @lauren5551,
which output did you get from Gecko? I suggest you generate a k-mer count database of each group of genomes by using meryl and comparing both sets in order to identify potential duplications.

A different approach could be to re-annotate each group by using maker and then comparing the annotation files with Parseval.

Never tried those methods before for analyzing duplications, but I think that can provide you an initial insight.