Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

agglomerative method in snpgdsHCluster #106

Open
botanicpanic1 opened this issue Jan 11, 2024 · 0 comments
Open

agglomerative method in snpgdsHCluster #106

botanicpanic1 opened this issue Jan 11, 2024 · 0 comments

Comments

@botanicpanic1
Copy link

I am using SNPRelate to produce a distance-based tree starting from a vcf file containing SNPs produced with ddRADseq.
I was curious to know which agglomerative method was employed in snpgdsHCluster and in the documentation is reported that: "Call the function hclust to perform hierarchical cluster analysis, using method="average"". So basically snpgdsHCluster uses UPGMA. But usually tree crafted using UPGMA should be ultrametric, however the output is an additive tree. Is there an explanation for this? Thanks to whoever will respond!

@botanicpanic1 botanicpanic1 changed the title agglomerative method in snpgdsHCluster and bootstrap agglomerative method in snpgdsHCluster Jan 11, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant