Fasttree - How To Remove Trifurcation Inside Tree?

Question

[onpelikan]

Hi, I'm using the MAPP program for protein mutations analysis. This program needs phylogenetic tree from multiple sequence alignment.

For tree construction I used FastTree. It is the most fast tool I have ever tried. But there is little problem with the tree it generates.

Inside the tree occurs trifurcation (one parent - three children). But MAPP program needs only two children inside the tree (root trifurcation is OK).

Do you know how to reformat the tree without change his phylogenetic meaning? Or is there any option (code change) in FastTree to solve this?

Thank you.

[Moses]

I'm having the same issue however its not because of duplicate sequences, its because FastTrree algorithm by default is assigning three children to the root, Is there an option that I can set so that FastTree will purely be a bifurcating tree all the way from root to the leaves?

Answer 1

[onpelikan]

Problem solved. I had to exclude duplicate sequences. Blast with nr database gave me for LacI repressor some duplicate sequences (duplicate by protein letter sequence not by name).