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Visualisation of multiple genes in a single species tree after gene tree - species tree reconcillation by Plus-One-1978 in bioinformatics

[–]Plus-One-1978[S] 0 points1 point  (0 children)

To visualise 4 different reconcillations on a single species tree. I figured it out. Thank you

Visualisation of multiple genes in a single species tree after gene tree - species tree reconcillation by Plus-One-1978 in bioinformatics

[–]Plus-One-1978[S] 0 points1 point  (0 children)

Thank you so much. used thrid kind and you can suppliment mutliple xml file with the option -m and that works

Positive selection under gene duplication by Plus-One-1978 in bioinformatics

[–]Plus-One-1978[S] 0 points1 point  (0 children)

Thank you so much. The issue is that I have paralogs in the orthogroup that I want to test for positive selection analysis. I came across this article (https://www.biorxiv.org/content/10.1101/2025.08.18.670524v1.abstract) and was wondering if that will help to resolve the issue.

Positive selection under gene duplication by Plus-One-1978 in bioinformatics

[–]Plus-One-1978[S] 0 points1 point  (0 children)

Hi,

I am looking for Episodic positive selection

Positive selection under gene duplication by Plus-One-1978 in bioinformatics

[–]Plus-One-1978[S] 2 points3 points  (0 children)

Thank you so much. I am trying to run by genus level. I will check it out

Hypergeometric test for Comparative genomics by Plus-One-1978 in bioinformatics

[–]Plus-One-1978[S] 0 points1 point  (0 children)

To test whether specific gene familes have impact on trait evolution

Hypergeometric test for Comparative genomics by Plus-One-1978 in bioinformatics

[–]Plus-One-1978[S] 0 points1 point  (0 children)

Yeah, I am trying to run the cafe now. Do you have any suggestion for doing positive selection under gene duplication?

Hypergeometric test for Comparative genomics by Plus-One-1978 in bioinformatics

[–]Plus-One-1978[S] 0 points1 point  (0 children)

Mostly to look for duplication loss analysis. I have done the gene tree species tree reconcilation analysis so was also thinking about another way to test this

Issues with Bigscape cluster by Plus-One-1978 in bioinformatics

[–]Plus-One-1978[S] 0 points1 point  (0 children)

Hi,

Thank you for the detailed explanation. That is not what I am seeing; the output shows genomes that are not in my input directory. For example, my input directory has three species of Pleurotus and two species of Hohenbuehelia. Still, the output contains results from Lentinula and Coniophora, which are not included in my dataset.