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

**URL:** <https://help.galaxyproject.org/t/not-sure-which-tool-to-use-for-genomic-comparison-any-suggestions/6283>\
**Category:** Uncategorized\
**Tags:** genome-annotation\
**Created:** [June 29, 2021, 11:13pm UTC](https://help.galaxyproject.org/t/not-sure-which-tool-to-use-for-genomic-comparison-any-suggestions/6283 "2021-06-29T23:13:51Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![lauren5551](https://avatars.discourse-cdn.com/v4/letter/l/b38774/32.png) [@lauren5551](https://help.galaxyproject.org/u/lauren5551)\
**Post date:** [June 29, 2021, 11:13pm UTC](https://help.galaxyproject.org/t/not-sure-which-tool-to-use-for-genomic-comparison-any-suggestions/6283/1 "2021-06-29T23:13:51Z")

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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

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**Author:** ![gallardoalba](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gallardoalba/32/1903_2.png) [@gallardoalba](https://help.galaxyproject.org/u/gallardoalba)\
**Post date:** [July 1, 2021, 7:41pm UTC](https://help.galaxyproject.org/t/not-sure-which-tool-to-use-for-genomic-comparison-any-suggestions/6283/2 "2021-07-01T19:41:09Z")

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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](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy2) and comparing both sets in order to identify potential duplications.

A different approach could be to re-annotate each group by using [maker](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11+galaxy1) and then comparing the annotation files with [Parseval](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0).

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

Regards.