About negative branches on NJ tree

[xiekunwhy]

Hi,

My question is not really aboat gotree, just want to know do you have any idea to deal with those negative distance branches on NJ tree?

Replace all negative value using 0, or all branches plus the smallest distances ?

Best,
Kun

[fredericlemoine]

Hi,

If it is required by your downstream analysis, you can replace negative branch lengths with 0:

gotree brlen setmin -l 0

However, it will potentially bias the distances between tips.