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Published 20 hours ago • verified publisher icon nickjcroucher

SNP counts on branches

Open nwheeler443 opened this issue 6 years ago • 2 comments

In the final_tree.tre output file produced by Gubbins, the branch labels that should be SNP counts are decimal numbers instead which don't match the numbers in the per_branch_statistics.csv file. Could someone please correct this?

nwheeler443 avatar Jul 25 '18 10:07 nwheeler443

Hi @simonrharris , could you comment on this please? I'm not entirely sure myself in which unit we measure the distances between the individual nodes.

puethe avatar Jul 30 '18 16:07 puethe

I suspect the branch lengths in the tree are just adjustments to the lengths in the likelihood tree whereas Nicole is asking for the count of reconstructed SNPs per branch, which seems sensible given the rest of the output.

simonrharris avatar Aug 06 '18 08:08 simonrharris