Hello, I have generated a VCF detailing the SNPs in 18 individuals from a population. In a pilot study, I had previously used some of the Genome Diversity tools to generate the genotypes for the samples and then visualized their relatedness to each other using a phylogenetic tree. I would like to d…

Hi @Danielle_Ireland The Genome Diversity tools have been deprecated for several years now (at least 5). The good news is that those were based on R packages that you can directly use in RStudio within Galaxy. Q&A (at the prior Galaxy biostars forum): RGenetics and Genome Diversity Bioconductor …

Hello Danielle, Maybe the answer from Jen can help you dealing with your issue coding inside Galaxy, but in case you are searching “classical”" Galaxy tools who can made the job, maybe you can give more informations about the “steps” you want to follow and/or what you have as input, what you want a…

Thank you @yvanlebras !! – those are the Genome Diversity tools :slight_smile: The EU server doesn’t have them marked as deprecated but I’m pretty sure there are some usage issues. @Danielle_Ireland You can certainly try the tools at EU – then if you run into problems, consider other options, includ…

Thank you @jennaj and @yvanlebras ! Yes, @yvanlebras those are the exact tools I had been using previously on usegalaxy and was hoping to use now. I had used them ~ 2 years ago and must not have realized they were deprecated at the time. I will try to move forward with the R packages to see if this …

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Is there anything available to replace the deprecated Genome Diversity tools

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