I am getting negative branches with the Neighbor-joining method, which I set to zero. However, I've read that I should transfer negative distances somewhere else and I do not know how. Does any have an script/method to transfer negative distances to the corresponding branches?. Thanks in advance for any help.
Ordinarily, with negative branch lengths, you would set the negative branch to zero, and then add the difference to the adjacent branch length so that the total distance between an adjacent pair of terminal nodes remains unaffected.
Cristian, thanks for your reply. I am doing just that using the following perl oneliner
perl -p -i.bk -e 's/-[0-9]*\.[0-9]*/0/g' outtree
However, negative distances that are set to zero should be add somewhere else in the tree but where and how. That was my question. Unfortunately the link you provided does not give me a solution.
Ordinarily, with negative branch lengths, you would set the negative branch to zero, and then add the difference to the adjacent branch length so that the total distance between an adjacent pair of terminal nodes remains unaffected.
Michael, thanks for your reply. I've just updated my version of dendroscope (great software) from version 1 to 3 and it seems that it does it all for me. At least,I do not see any branch going in opposite direction to the adjacent branch.
- Badges
- Science method
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics
- Phylogenetic Analysis